diff --git a/ql/lib/codeql/actions/Ast.qll b/ql/lib/codeql/actions/Ast.qll
index cc29ceffe53..620f74e25bb 100644
--- a/ql/lib/codeql/actions/Ast.qll
+++ b/ql/lib/codeql/actions/Ast.qll
@@ -22,6 +22,10 @@ class AstNode instanceof AstNodeImpl {
   CompositeAction getEnclosingCompositeAction() { result = super.getEnclosingCompositeAction() }
 
   Expression getInScopeEnvVarExpr(string name) { result = super.getInScopeEnvVarExpr(name) }
+
+  ScalarValue getInScopeDefaultValue(string name, string prop) {
+    result = super.getInScopeDefaultValue(name, prop)
+  }
 }
 
 class ScalarValue extends AstNode instanceof ScalarValueImpl {
@@ -121,6 +125,10 @@ class ReusableWorkflow extends Workflow instanceof ReusableWorkflowImpl {
 
 class Input extends AstNode instanceof InputImpl { }
 
+class Default extends AstNode instanceof DefaultsImpl {
+  ScalarValue getValue(string name, string prop) { result = super.getValue(name, prop) }
+}
+
 class Outputs extends AstNode instanceof OutputsImpl {
   Expression getAnOutputExpr() { result = super.getAnOutputExpr() }
 
@@ -286,14 +294,18 @@ class ExternalJob extends Job, Uses instanceof ExternalJobImpl { }
  * See https://docs.github.com/en/free-pro-team@latest/actions/reference/workflow-syntax-for-github-actions#jobsjob_idstepsrun.
  */
 class Run extends Step instanceof RunImpl {
-  string getScript() { result = super.getScript() }
-
-  ScalarValue getScriptScalar() { result = super.getScriptScalar() }
+  ShellScript getScript() { result = super.getScript() }
 
   Expression getAnScriptExpr() { result = super.getAnScriptExpr() }
 
   string getWorkingDirectory() { result = super.getWorkingDirectory() }
 
+  string getShell() { result = super.getShell() }
+}
+
+class ShellScript extends ScalarValueImpl instanceof ShellScriptImpl {
+  string getRawScript() { result = super.getRawScript() }
+
   string getStmt(int i) { result = super.getStmt(i) }
 
   string getAStmt() { result = super.getAStmt() }
@@ -302,19 +314,23 @@ class Run extends Step instanceof RunImpl {
 
   string getACommand() { result = super.getACommand() }
 
-  predicate getAssignment(int i, string name, string value) { super.getAssignment(i, name, value) }
+  string getFileReadCommand(int i) { result = super.getFileReadCommand(i) }
 
-  predicate getAnAssignment(string name, string value) { super.getAnAssignment(name, value) }
+  string getAFileReadCommand() { result = super.getAFileReadCommand() }
 
-  predicate getAWriteToGitHubEnv(string name, string value) {
-    super.getAWriteToGitHubEnv(name, value)
+  predicate getAssignment(int i, string name, string data) { super.getAssignment(i, name, data) }
+
+  predicate getAnAssignment(string name, string data) { super.getAnAssignment(name, data) }
+
+  predicate getAWriteToGitHubEnv(string name, string data) {
+    super.getAWriteToGitHubEnv(name, data)
   }
 
-  predicate getAWriteToGitHubOutput(string name, string value) {
-    super.getAWriteToGitHubOutput(name, value)
+  predicate getAWriteToGitHubOutput(string name, string data) {
+    super.getAWriteToGitHubOutput(name, data)
   }
 
-  predicate getAWriteToGitHubPath(string value) { super.getAWriteToGitHubPath(value) }
+  predicate getAWriteToGitHubPath(string data) { super.getAWriteToGitHubPath(data) }
 
   predicate getAnEnvReachingGitHubOutputWrite(string var, string output_field) {
     super.getAnEnvReachingGitHubOutputWrite(var, output_field)
@@ -331,6 +347,18 @@ class Run extends Step instanceof RunImpl {
   predicate getACmdReachingGitHubEnvWrite(string cmd, string output_field) {
     super.getACmdReachingGitHubEnvWrite(cmd, output_field)
   }
+
+  predicate getAnEnvReachingGitHubPathWrite(string var) {
+    super.getAnEnvReachingGitHubPathWrite(var)
+  }
+
+  predicate getACmdReachingGitHubPathWrite(string cmd) { super.getACmdReachingGitHubPathWrite(cmd) }
+
+  predicate fileToGitHubEnv(string path) { super.fileToGitHubEnv(path) }
+
+  predicate fileToGitHubOutput(string path) { super.fileToGitHubOutput(path) }
+
+  predicate fileToGitHubPath(string path) { super.fileToGitHubPath(path) }
 }
 
 abstract class SimpleReferenceExpression extends AstNode instanceof SimpleReferenceExpressionImpl {
diff --git a/ql/lib/codeql/actions/Bash.qll b/ql/lib/codeql/actions/Bash.qll
index fc9a75319eb..541ab437db2 100644
--- a/ql/lib/codeql/actions/Bash.qll
+++ b/ql/lib/codeql/actions/Bash.qll
@@ -1,7 +1,303 @@
 private import codeql.actions.Ast
-private import codeql.Locations
-import codeql.actions.config.Config
-private import codeql.actions.security.ControlChecks
+
+class BashShellScript extends ShellScript {
+  BashShellScript() {
+    exists(Run run |
+      this = run.getScript() and
+      run.getShell().matches("bash%")
+    )
+  }
+
+  private string lineProducer(int i) {
+    result = this.getRawScript().regexpReplaceAll("\\\\\\s*\n", "").splitAt("\n", i)
+  }
+
+  private predicate cmdSubstitutionReplacement(string cmdSubs, string id, int k) {
+    exists(string line | line = this.lineProducer(k) |
+      exists(int i, int j |
+        cmdSubs =
+          // $() cmd substitution
+          line.regexpFind("\\$\\((?:[^()]+|\\((?:[^()]+|\\([^()]*\\))*\\))*\\)", i, j)
+              .regexpReplaceAll("^\\$\\(", "")
+              .regexpReplaceAll("\\)$", "") and
+        id = "cmdsubs:" + k + ":" + i + ":" + j
+      )
+      or
+      exists(int i, int j |
+        // `...` cmd substitution
+        cmdSubs =
+          line.regexpFind("\\`[^\\`]+\\`", i, j)
+              .regexpReplaceAll("^\\`", "")
+              .regexpReplaceAll("\\`$", "") and
+        id = "cmd:" + k + ":" + i + ":" + j
+      )
+    )
+  }
+
+  private predicate rankedCmdSubstitutionReplacements(int i, string old, string new) {
+    old = rank[i](string old2 | this.cmdSubstitutionReplacement(old2, _, _) | old2) and
+    this.cmdSubstitutionReplacement(old, new, _)
+  }
+
+  private predicate doReplaceCmdSubstitutions(int line, int round, string old, string new) {
+    round = 0 and
+    old = this.lineProducer(line) and
+    new = old
+    or
+    round > 0 and
+    exists(string middle, string target, string replacement |
+      this.doReplaceCmdSubstitutions(line, round - 1, old, middle) and
+      this.rankedCmdSubstitutionReplacements(round, target, replacement) and
+      new = middle.replaceAll(target, replacement)
+    )
+  }
+
+  private string cmdSubstitutedLineProducer(int i) {
+    // script lines where any command substitution has been replaced with a unique placeholder
+    result =
+      max(int round, string new |
+        this.doReplaceCmdSubstitutions(i, round, _, new)
+      |
+        new order by round
+      )
+    or
+    this.cmdSubstitutionReplacement(result, _, i)
+  }
+
+  private predicate quotedStringReplacement(string quotedStr, string id) {
+    exists(string line, int k | line = this.cmdSubstitutedLineProducer(k) |
+      exists(int i, int j |
+        // double quoted string
+        quotedStr = line.regexpFind("\"((?:[^\"\\\\]|\\\\.)*)\"", i, j) and
+        id =
+          "qstr:" + k + ":" + i + ":" + j + ":" + quotedStr.length() + ":" +
+            quotedStr.regexpReplaceAll("[^a-zA-Z0-9]", "")
+      )
+      or
+      exists(int i, int j |
+        // single quoted string
+        quotedStr = line.regexpFind("'((?:\\\\.|[^'\\\\])*)'", i, j) and
+        id =
+          "qstr:" + k + ":" + i + ":" + j + ":" + quotedStr.length() + ":" +
+            quotedStr.regexpReplaceAll("[^a-zA-Z0-9]", "")
+      )
+    )
+  }
+
+  private predicate rankedQuotedStringReplacements(int i, string old, string new) {
+    old = rank[i](string old2 | this.quotedStringReplacement(old2, _) | old2) and
+    this.quotedStringReplacement(old, new)
+  }
+
+  private predicate doReplaceQuotedStrings(int line, int round, string old, string new) {
+    round = 0 and
+    old = this.cmdSubstitutedLineProducer(line) and
+    new = old
+    or
+    round > 0 and
+    exists(string middle, string target, string replacement |
+      this.doReplaceQuotedStrings(line, round - 1, old, middle) and
+      this.rankedQuotedStringReplacements(round, target, replacement) and
+      new = middle.replaceAll(target, replacement)
+    )
+  }
+
+  private string quotedStringLineProducer(int i) {
+    result =
+      max(int round, string new | this.doReplaceQuotedStrings(i, round, _, new) | new order by round)
+  }
+
+  private string stmtProducer(int i) {
+    result = this.quotedStringLineProducer(i).splitAt(Bash::splitSeparator()).trim() and
+    // when splitting the line with a separator that is not present, the result is the original line which may contain other separators
+    // we only one the split parts that do not contain any of the separators
+    not result.indexOf(Bash::splitSeparator()) > -1
+  }
+
+  private predicate doStmtRestoreQuotedStrings(int line, int round, string old, string new) {
+    round = 0 and
+    old = this.stmtProducer(line) and
+    new = old
+    or
+    round > 0 and
+    exists(string middle, string target, string replacement |
+      this.doStmtRestoreQuotedStrings(line, round - 1, old, middle) and
+      this.rankedQuotedStringReplacements(round, target, replacement) and
+      new = middle.replaceAll(replacement, target)
+    )
+  }
+
+  private string restoredStmtQuotedStringLineProducer(int i) {
+    result =
+      max(int round, string new |
+        this.doStmtRestoreQuotedStrings(i, round, _, new)
+      |
+        new order by round
+      )
+  }
+
+  private predicate doStmtRestoreCmdSubstitutions(int line, int round, string old, string new) {
+    round = 0 and
+    old = this.restoredStmtQuotedStringLineProducer(line) and
+    new = old
+    or
+    round > 0 and
+    exists(string middle, string target, string replacement |
+      this.doStmtRestoreCmdSubstitutions(line, round - 1, old, middle) and
+      this.rankedCmdSubstitutionReplacements(round, target, replacement) and
+      new = middle.replaceAll(replacement, target)
+    )
+  }
+
+  override string getStmt(int i) {
+    result =
+      max(int round, string new |
+        this.doStmtRestoreCmdSubstitutions(i, round, _, new)
+      |
+        new order by round
+      )
+  }
+
+  override string getAStmt() { result = this.getStmt(_) }
+
+  private string cmdProducer(int i) {
+    result = this.quotedStringLineProducer(i).splitAt(Bash::separator()).trim() and
+    // when splitting the line with a separator that is not present, the result is the original line which may contain other separators
+    // we only one the split parts that do not contain any of the separators
+    not result.indexOf(Bash::separator()) > -1
+  }
+
+  private predicate doCmdRestoreQuotedStrings(int line, int round, string old, string new) {
+    round = 0 and
+    old = this.cmdProducer(line) and
+    new = old
+    or
+    round > 0 and
+    exists(string middle, string target, string replacement |
+      this.doCmdRestoreQuotedStrings(line, round - 1, old, middle) and
+      this.rankedQuotedStringReplacements(round, target, replacement) and
+      new = middle.replaceAll(replacement, target)
+    )
+  }
+
+  private string restoredCmdQuotedStringLineProducer(int i) {
+    result =
+      max(int round, string new |
+        this.doCmdRestoreQuotedStrings(i, round, _, new)
+      |
+        new order by round
+      )
+  }
+
+  private predicate doCmdRestoreCmdSubstitutions(int line, int round, string old, string new) {
+    round = 0 and
+    old = this.restoredCmdQuotedStringLineProducer(line) and
+    new = old
+    or
+    round > 0 and
+    exists(string middle, string target, string replacement |
+      this.doCmdRestoreCmdSubstitutions(line, round - 1, old, middle) and
+      this.rankedCmdSubstitutionReplacements(round, target, replacement) and
+      new = middle.replaceAll(replacement, target)
+    )
+  }
+
+  string getCmd(int i) {
+    result =
+      max(int round, string new |
+        this.doCmdRestoreCmdSubstitutions(i, round, _, new)
+      |
+        new order by round
+      )
+  }
+
+  string getACmd() { result = this.getCmd(_) }
+
+  override string getCommand(int i) {
+    result = this.getCmd(i) and
+    // exclude variable declarations
+    not result.regexpMatch("^[a-zA-Z0-9\\-_]+=") and
+    // exclude the following keywords
+    not result =
+      [
+        "", "for", "in", "do", "done", "if", "then", "else", "elif", "fi", "while", "until", "case",
+        "esac", "{", "}"
+      ]
+  }
+
+  override string getACommand() { result = this.getCommand(_) }
+
+  override string getFileReadCommand(int i) {
+    result = this.getStmt(i) and
+    result.matches(Bash::fileReadCommand() + "%")
+  }
+
+  override string getAFileReadCommand() { result = this.getFileReadCommand(_) }
+
+  override predicate getAssignment(int i, string name, string data) {
+    exists(string stmt |
+      stmt = this.getStmt(i) and
+      name = stmt.regexpCapture("^([a-zA-Z0-9\\-_]+)=.*", 1) and
+      data = stmt.regexpCapture("^[a-zA-Z0-9\\-_]+=(.*)", 1)
+    )
+  }
+
+  override predicate getAnAssignment(string name, string data) { this.getAssignment(_, name, data) }
+
+  override predicate getAWriteToGitHubEnv(string name, string data) {
+    exists(string raw |
+      Bash::extractFileWrite(this.getRawScript(), "GITHUB_ENV", raw) and
+      Bash::extractVariableAndValue(raw, name, data)
+    )
+  }
+
+  override predicate getAWriteToGitHubOutput(string name, string data) {
+    exists(string raw |
+      Bash::extractFileWrite(this.getRawScript(), "GITHUB_OUTPUT", raw) and
+      Bash::extractVariableAndValue(raw, name, data)
+    )
+  }
+
+  override predicate getAWriteToGitHubPath(string data) {
+    Bash::extractFileWrite(this.getRawScript(), "GITHUB_PATH", data)
+  }
+
+  override predicate getAnEnvReachingGitHubOutputWrite(string var, string output_field) {
+    Bash::envReachingGitHubFileWrite(this, var, "GITHUB_OUTPUT", output_field)
+  }
+
+  override predicate getACmdReachingGitHubOutputWrite(string cmd, string output_field) {
+    Bash::cmdReachingGitHubFileWrite(this, cmd, "GITHUB_OUTPUT", output_field)
+  }
+
+  override predicate getAnEnvReachingGitHubEnvWrite(string var, string output_field) {
+    Bash::envReachingGitHubFileWrite(this, var, "GITHUB_ENV", output_field)
+  }
+
+  override predicate getACmdReachingGitHubEnvWrite(string cmd, string output_field) {
+    Bash::cmdReachingGitHubFileWrite(this, cmd, "GITHUB_ENV", output_field)
+  }
+
+  override predicate getAnEnvReachingGitHubPathWrite(string var) {
+    Bash::envReachingGitHubFileWrite(this, var, "GITHUB_PATH", _)
+  }
+
+  override predicate getACmdReachingGitHubPathWrite(string cmd) {
+    Bash::cmdReachingGitHubFileWrite(this, cmd, "GITHUB_PATH", _)
+  }
+
+  override predicate fileToGitHubEnv(string path) {
+    Bash::fileToFileWrite(this, "GITHUB_ENV", path)
+  }
+
+  override predicate fileToGitHubOutput(string path) {
+    Bash::fileToFileWrite(this, "GITHUB_OUTPUT", path)
+  }
+
+  override predicate fileToGitHubPath(string path) {
+    Bash::fileToFileWrite(this, "GITHUB_PATH", path)
+  }
+}
 
 module Bash {
   string stmtSeparator() { result = ";" }
@@ -23,7 +319,7 @@ module Bash {
     result = pipeSeparator()
   }
 
-  string partialFileContentCommand() { result = ["cat", "jq", "yq", "tail", "head"] }
+  string fileReadCommand() { result = ["<", "cat", "jq", "yq", "tail", "head"] }
 
   /** Checks if expr is a bash command substitution */
   bindingset[expr]
@@ -133,8 +429,7 @@ module Bash {
     string script, string cmd, string file, string content, string filters
   ) {
     exists(string regexp |
-      regexp =
-        "(?i)(echo|printf|write-output)\\s*(.*?)\\s*(>>|>|\\s*\\|\\s*tee\\s*(-a|--append)?)\\s*(\\S+)" and
+      regexp = "(?i)(echo|printf)\\s*(.*?)\\s*(>>|>|\\s*\\|\\s*tee\\s*(-a|--append)?)\\s*(\\S+)" and
       cmd = script.regexpCapture(regexp, 1) and
       file = trimQuotes(script.regexpCapture(regexp, 5)) and
       filters = "" and
@@ -145,13 +440,12 @@ module Bash {
   bindingset[script]
   predicate singleLineWorkflowCmd(string script, string cmd, string key, string value) {
     exists(string regexp |
-      regexp =
-        "(?i)(echo|printf|write-output)\\s*(['|\"])?::(set-[a-z]+)\\s*name\\s*=\\s*(.*?)::(.*)" and
+      regexp = "(?i)(echo|printf)\\s*(['|\"])?::(set-[a-z]+)\\s*name\\s*=\\s*(.*?)::(.*)" and
       cmd = script.regexpCapture(regexp, 3) and
       key = script.regexpCapture(regexp, 4) and
       value = trimQuotes(script.regexpCapture(regexp, 5))
       or
-      regexp = "(?i)(echo|printf|write-output)\\s*(['|\"])?::(add-[a-z]+)\\s*::(.*)" and
+      regexp = "(?i)(echo|printf)\\s*(['|\"])?::(add-[a-z]+)\\s*::(.*)" and
       cmd = script.regexpCapture(regexp, 3) and
       key = "" and
       value = trimQuotes(script.regexpCapture(regexp, 4))
@@ -262,57 +556,38 @@ module Bash {
   }
 
   /** Writes the content of the file specified by `path` into a file pointed to by `file_var` */
-  predicate fileToFileWrite(Run run, string file_var, string path) {
+  predicate fileToFileWrite(BashShellScript script, string file_var, string path) {
     exists(string regexp, string stmt, string file_expr |
       regexp =
         "(?i)(cat)\\s*" + "((?:(?!<<|<<-)[^>\n])+)\\s*" +
           "(>>|>|\\s*\\|\\s*tee\\s*(-a|--append)?)\\s*" + "(\\S+)" and
-      stmt = run.getAStmt() and
+      stmt = script.getAStmt() and
       file_expr = trimQuotes(stmt.regexpCapture(regexp, 5)) and
       path = stmt.regexpCapture(regexp, 2) and
       containsParameterExpansion(file_expr, file_var, _, _)
     )
   }
 
-  predicate fileToGitHubEnv(Run run, string path) { fileToFileWrite(run, "GITHUB_ENV", path) }
-
-  predicate fileToGitHubOutput(Run run, string path) { fileToFileWrite(run, "GITHUB_OUTPUT", path) }
-
-  predicate fileToGitHubPath(Run run, string path) { fileToFileWrite(run, "GITHUB_PATH", path) }
-
-  bindingset[snippet]
-  predicate outputsPartialFileContent(Run run, string snippet) {
-    // e.g.
-    // echo FOO=`yq '.foo' foo.yml` >> $GITHUB_ENV
-    // echo "FOO=$(<foo.txt)" >> $GITHUB_ENV
-    // yq '.foo' foo.yml >> $GITHUB_PATH
-    // cat foo.txt >> $GITHUB_PATH
-    exists(int i, string line, string cmd |
-      run.getStmt(i) = line and
-      line.indexOf(snippet.regexpReplaceAll("^\\$\\(", "").regexpReplaceAll("\\)$", "")) > -1 and
-      run.getCommand(i) = cmd and
-      cmd.indexOf(["<", Bash::partialFileContentCommand() + " "]) = 0
-    )
-  }
-
   /**
    * Holds if the Run scripts contains an access to an environment variable called `var`
    * which value may get appended to the GITHUB_XXX special file
    */
-  predicate envReachingGitHubFileWrite(Run run, string var, string file_var, string field) {
+  predicate envReachingGitHubFileWrite(
+    BashShellScript script, string var, string file_var, string field
+  ) {
     exists(string file_write_value |
       (
         file_var = "GITHUB_ENV" and
-        run.getAWriteToGitHubEnv(field, file_write_value)
+        script.getAWriteToGitHubEnv(field, file_write_value)
         or
         file_var = "GITHUB_OUTPUT" and
-        run.getAWriteToGitHubOutput(field, file_write_value)
+        script.getAWriteToGitHubOutput(field, file_write_value)
         or
         file_var = "GITHUB_PATH" and
         field = "PATH" and
-        run.getAWriteToGitHubPath(file_write_value)
+        script.getAWriteToGitHubPath(file_write_value)
       ) and
-      envReachingRunExpr(run, var, file_write_value)
+      envReachingRunExpr(script, var, file_write_value)
     )
   }
 
@@ -321,11 +596,11 @@ module Bash {
    * Where the expression is a string captured from the Run's script.
    */
   bindingset[expr]
-  predicate envReachingRunExpr(Run run, string var, string expr) {
+  predicate envReachingRunExpr(BashShellScript script, string var, string expr) {
     exists(string var2, string value2 |
       // VAR2=${VAR:-default} (var2=value2)
       // echo "FIELD=${VAR2:-default}" >> $GITHUB_ENV (field, file_write_value)
-      run.getAnAssignment(var2, value2) and
+      script.getAnAssignment(var2, value2) and
       containsParameterExpansion(value2, var, _, _) and
       containsParameterExpansion(expr, var2, _, _)
     )
@@ -339,33 +614,42 @@ module Bash {
    * Holds if the Run scripts contains a command substitution (`cmd`)
    * which output may get appended to the GITHUB_XXX special file
    */
-  predicate cmdReachingGitHubFileWrite(Run run, string cmd, string file_var, string field) {
+  predicate cmdReachingGitHubFileWrite(
+    BashShellScript script, string cmd, string file_var, string field
+  ) {
     exists(string file_write_value |
       (
         file_var = "GITHUB_ENV" and
-        run.getAWriteToGitHubEnv(field, file_write_value)
+        script.getAWriteToGitHubEnv(field, file_write_value)
         or
         file_var = "GITHUB_OUTPUT" and
-        run.getAWriteToGitHubOutput(field, file_write_value)
+        script.getAWriteToGitHubOutput(field, file_write_value)
         or
         file_var = "GITHUB_PATH" and
         field = "PATH" and
-        run.getAWriteToGitHubPath(file_write_value)
+        script.getAWriteToGitHubPath(file_write_value)
       ) and
-      (
-        // cmd output is assigned to a second variable (var2) and var2 reaches the file write
-        exists(string var2, string value2 |
-          // VAR2=$(cmd)
-          // echo "FIELD=${VAR2:-default}" >> $GITHUB_ENV (field, file_write_value)
-          run.getAnAssignment(var2, value2) and
-          containsCmdSubstitution(value2, cmd) and
-          containsParameterExpansion(file_write_value, var2, _, _)
-        )
-        or
-        // var reaches the file write directly
-        // echo "FIELD=$(cmd)" >> $GITHUB_ENV (field, file_write_value)
-        containsCmdSubstitution(file_write_value, cmd)
-      )
+      cmdReachingRunExpr(script, cmd, file_write_value)
     )
   }
+
+  /**
+   * Holds if a command output is used, directly or indirectly, in a Run's step expression.
+   * Where the expression is a string captured from the Run's script.
+   */
+  bindingset[expr]
+  predicate cmdReachingRunExpr(BashShellScript script, string cmd, string expr) {
+    // cmd output is assigned to a second variable (var2) and var2 reaches the file write
+    exists(string var2, string value2 |
+      // VAR2=$(cmd)
+      // echo "FIELD=${VAR2:-default}" >> $GITHUB_ENV (field, file_write_value)
+      script.getAnAssignment(var2, value2) and
+      containsCmdSubstitution(value2, cmd) and
+      containsParameterExpansion(expr, var2, _, _)
+    )
+    or
+    // var reaches the file write directly
+    // echo "FIELD=$(cmd)" >> $GITHUB_ENV (field, file_write_value)
+    containsCmdSubstitution(expr, cmd)
+  }
 }
diff --git a/ql/lib/codeql/actions/Helper.qll b/ql/lib/codeql/actions/Helper.qll
index ae4405a185b..fb6fdf2d74b 100644
--- a/ql/lib/codeql/actions/Helper.qll
+++ b/ql/lib/codeql/actions/Helper.qll
@@ -3,6 +3,7 @@ private import codeql.Locations
 private import codeql.actions.security.ControlChecks
 import codeql.actions.config.Config
 import codeql.actions.Bash
+import codeql.actions.PowerShell
 
 bindingset[expr]
 string normalizeExpr(string expr) {
diff --git a/ql/lib/codeql/actions/PowerShell.qll b/ql/lib/codeql/actions/PowerShell.qll
new file mode 100644
index 00000000000..1727930c2a3
--- /dev/null
+++ b/ql/lib/codeql/actions/PowerShell.qll
@@ -0,0 +1,50 @@
+private import codeql.actions.Ast
+
+class PowerShellScript extends ShellScript {
+  PowerShellScript() {
+    exists(Run run |
+      this = run.getScript() and
+      run.getShell().matches("pwsh%")
+    )
+  }
+
+  override string getStmt(int i) { none() }
+
+  override string getAStmt() { none() }
+
+  override string getCommand(int i) { none() }
+
+  override string getACommand() { none() }
+
+  override string getFileReadCommand(int i) { none() }
+
+  override string getAFileReadCommand() { none() }
+
+  override predicate getAssignment(int i, string name, string data) { none() }
+
+  override predicate getAnAssignment(string name, string data) { none() }
+
+  override predicate getAWriteToGitHubEnv(string name, string data) { none() }
+
+  override predicate getAWriteToGitHubOutput(string name, string data) { none() }
+
+  override predicate getAWriteToGitHubPath(string data) { none() }
+
+  override predicate getAnEnvReachingGitHubOutputWrite(string var, string output_field) { none() }
+
+  override predicate getACmdReachingGitHubOutputWrite(string cmd, string output_field) { none() }
+
+  override predicate getAnEnvReachingGitHubEnvWrite(string var, string output_field) { none() }
+
+  override predicate getACmdReachingGitHubEnvWrite(string cmd, string output_field) { none() }
+
+  override predicate getAnEnvReachingGitHubPathWrite(string var) { none() }
+
+  override predicate getACmdReachingGitHubPathWrite(string cmd) { none() }
+
+  override predicate fileToGitHubEnv(string path) { none() }
+
+  override predicate fileToGitHubOutput(string path) { none() }
+
+  override predicate fileToGitHubPath(string path) { none() }
+}
diff --git a/ql/lib/codeql/actions/ast/internal/Ast.qll b/ql/lib/codeql/actions/ast/internal/Ast.qll
index eaf1ae871a9..43772a978c5 100644
--- a/ql/lib/codeql/actions/ast/internal/Ast.qll
+++ b/ql/lib/codeql/actions/ast/internal/Ast.qll
@@ -62,6 +62,7 @@ private newtype TAstNode =
     n.lookup("jobs") instanceof YamlMapping
   } or
   TRunsNode(YamlMapping n) { exists(CompositeActionImpl a | a.getNode().lookup("runs") = n) } or
+  TDefaultsNode(YamlMapping n) { exists(YamlMapping m | m.lookup("defaults") = n) } or
   TInputsNode(YamlMapping n) { exists(YamlMapping m | m.lookup("inputs") = n) } or
   TInputNode(YamlValue n) { exists(YamlMapping m | m.lookup("inputs").(YamlMapping).maps(n, _)) } or
   TOutputsNode(YamlMapping n) { exists(YamlMapping m | m.lookup("outputs") = n) } or
@@ -141,6 +142,19 @@ abstract class AstNodeImpl extends TAstNode {
       env.getParentNode().getAChildNode*() = this
     )
   }
+
+  ScalarValueImpl getInScopeDefaultValue(string name, string prop) {
+    exists(DefaultsImpl dft |
+      this.getEnclosingJob().getNode().(YamlMapping).maps(_, dft.getNode()) and
+      result = dft.getValue(name, prop)
+    )
+    or
+    not exists(DefaultsImpl dft | this.getEnclosingJob() = dft.getParentNode()) and
+    exists(DefaultsImpl dft |
+      this.getEnclosingWorkflow().getNode().(YamlMapping).maps(_, dft.getNode()) and
+      result = dft.getValue(name, prop)
+    )
+  }
 }
 
 class ScalarValueImpl extends AstNodeImpl, TScalarValueNode {
@@ -165,6 +179,61 @@ class ScalarValueImpl extends AstNodeImpl, TScalarValueNode {
   string getValue() { result = value.getValue() }
 }
 
+class ShellScriptImpl extends ScalarValueImpl {
+  ShellScriptImpl() { exists(YamlMapping run | run.lookup("run").(YamlScalar) = this.getNode()) }
+
+  string getRawScript() { result = this.getValue().regexpReplaceAll("\\\\\\s*\n", "") }
+
+  RunImpl getEnclosingRun() { result.getNode().lookup("run") = this.getNode() }
+
+  abstract string getStmt(int i);
+
+  abstract string getAStmt();
+
+  abstract string getCommand(int i);
+
+  string getACommand() {
+    if this.getEnclosingRun().getShell().matches("bash%")
+    then result = this.(BashShellScript).getACommand()
+    else
+      if this.getEnclosingRun().getShell().matches("pwsh%")
+      then result = this.(PowerShellScript).getACommand()
+      else result = "NOT IMPLEMENTED"
+  }
+
+  abstract string getFileReadCommand(int i);
+
+  abstract string getAFileReadCommand();
+
+  abstract predicate getAssignment(int i, string name, string data);
+
+  abstract predicate getAnAssignment(string name, string data);
+
+  abstract predicate getAWriteToGitHubEnv(string name, string data);
+
+  abstract predicate getAWriteToGitHubOutput(string name, string data);
+
+  abstract predicate getAWriteToGitHubPath(string data);
+
+  abstract predicate getAnEnvReachingGitHubOutputWrite(string var, string output_field);
+
+  abstract predicate getACmdReachingGitHubOutputWrite(string cmd, string output_field);
+
+  abstract predicate getAnEnvReachingGitHubEnvWrite(string var, string output_field);
+
+  abstract predicate getACmdReachingGitHubEnvWrite(string cmd, string output_field);
+
+  abstract predicate getAnEnvReachingGitHubPathWrite(string var);
+
+  abstract predicate getACmdReachingGitHubPathWrite(string cmd);
+
+  abstract predicate fileToGitHubEnv(string path);
+
+  abstract predicate fileToGitHubOutput(string path);
+
+  abstract predicate fileToGitHubPath(string path);
+}
+
 class ExpressionImpl extends AstNodeImpl, TExpressionNode {
   YamlNode key;
   YamlString value;
@@ -493,6 +562,28 @@ class InputsImpl extends AstNodeImpl, TInputsNode {
   }
 }
 
+class DefaultsImpl extends AstNodeImpl, TDefaultsNode {
+  YamlMapping n;
+
+  DefaultsImpl() { this = TDefaultsNode(n) }
+
+  override string toString() { result = n.toString() }
+
+  override AstNodeImpl getAChildNode() { result.getNode() = n.getAChildNode*() }
+
+  override AstNodeImpl getParentNode() { result.getAChildNode() = this }
+
+  override string getAPrimaryQlClass() { result = "DefaultsImpl" }
+
+  override Location getLocation() { result = n.getLocation() }
+
+  override YamlMapping getNode() { result = n }
+
+  ScalarValueImpl getValue(string name, string prop) {
+    n.lookup(name).(YamlMapping).lookup(prop) = result.getNode()
+  }
+}
+
 class InputImpl extends AstNodeImpl, TInputNode {
   YamlValue n;
 
@@ -1314,20 +1405,18 @@ class ExternalJobImpl extends JobImpl, UsesImpl {
 
 class RunImpl extends StepImpl {
   YamlScalar script;
+  ScalarValueImpl scriptScalar;
 
-  RunImpl() { this.getNode().lookup("run") = script }
-
-  string getScript() { result = script.getValue().regexpReplaceAll("\\\\\\s*\n", "") }
-
-  ScalarValueImpl getScriptScalar() { result = TScalarValueNode(script) }
-
-  ExpressionImpl getAnScriptExpr() { result.getParentNode().getNode() = script }
+  RunImpl() {
+    this.getNode().lookup("run") = script and
+    scriptScalar = TScalarValueNode(script)
+  }
 
   override string toString() {
     if exists(this.getId()) then result = "Run Step: " + this.getId() else result = "Run Step"
   }
 
-  /** Gets the working directory for this `runs` mapping. */
+  /** Gets the working directory for this `run` mapping. */
   string getWorkingDirectory() {
     if exists(n.lookup("working-directory").(YamlString).getValue())
     then
@@ -1339,268 +1428,19 @@ class RunImpl extends StepImpl {
     else result = "GITHUB_WORKSPACE/"
   }
 
-  private string lineProducer(int i) {
-    result = script.getValue().regexpReplaceAll("\\\\\\s*\n", "").splitAt("\n", i)
+  /** Gets the shell for this `run` mapping. */
+  string getShell() {
+    if exists(n.lookup("shell").(YamlString).getValue())
+    then result = n.lookup("shell").(YamlString).getValue()
+    else
+      if exists(this.getInScopeDefaultValue("run", "shell"))
+      then result = this.getInScopeDefaultValue("run", "shell").getValue()
+      else result = "bash"
   }
 
-  private predicate cmdSubstitutionReplacement(string cmdSubs, string id, int k) {
-    exists(string line | line = this.lineProducer(k) |
-      exists(int i, int j |
-        cmdSubs =
-          // $() cmd substitution
-          line.regexpFind("\\$\\((?:[^()]+|\\((?:[^()]+|\\([^()]*\\))*\\))*\\)", i, j)
-              .regexpReplaceAll("^\\$\\(", "")
-              .regexpReplaceAll("\\)$", "") and
-        id = "cmdsubs:" + k + ":" + i + ":" + j
-      )
-      or
-      exists(int i, int j |
-        // `...` cmd substitution
-        cmdSubs =
-          line.regexpFind("\\`[^\\`]+\\`", i, j)
-              .regexpReplaceAll("^\\`", "")
-              .regexpReplaceAll("\\`$", "") and
-        id = "cmd:" + k + ":" + i + ":" + j
-      )
-    )
-  }
+  ShellScriptImpl getScript() { result = scriptScalar }
 
-  private predicate rankedCmdSubstitutionReplacements(int i, string old, string new) {
-    old = rank[i](string old2 | this.cmdSubstitutionReplacement(old2, _, _) | old2) and
-    this.cmdSubstitutionReplacement(old, new, _)
-  }
-
-  private predicate doReplaceCmdSubstitutions(int line, int round, string old, string new) {
-    round = 0 and
-    old = this.lineProducer(line) and
-    new = old
-    or
-    round > 0 and
-    exists(string middle, string target, string replacement |
-      this.doReplaceCmdSubstitutions(line, round - 1, old, middle) and
-      this.rankedCmdSubstitutionReplacements(round, target, replacement) and
-      new = middle.replaceAll(target, replacement)
-    )
-  }
-
-  private string cmdSubstitutedLineProducer(int i) {
-    // script lines where any command substitution has been replaced with a unique placeholder
-    result =
-      max(int round, string new |
-        this.doReplaceCmdSubstitutions(i, round, _, new)
-      |
-        new order by round
-      )
-    or
-    this.cmdSubstitutionReplacement(result, _, i)
-  }
-
-  private predicate quotedStringReplacement(string quotedStr, string id) {
-    exists(string line, int k | line = this.cmdSubstitutedLineProducer(k) |
-      exists(int i, int j |
-        // double quoted string
-        quotedStr = line.regexpFind("\"((?:[^\"\\\\]|\\\\.)*)\"", i, j) and
-        id =
-          "qstr:" + k + ":" + i + ":" + j + ":" + quotedStr.length() + ":" +
-            quotedStr.regexpReplaceAll("[^a-zA-Z0-9]", "")
-      )
-      or
-      exists(int i, int j |
-        // single quoted string
-        quotedStr = line.regexpFind("'((?:\\\\.|[^'\\\\])*)'", i, j) and
-        id =
-          "qstr:" + k + ":" + i + ":" + j + ":" + quotedStr.length() + ":" +
-            quotedStr.regexpReplaceAll("[^a-zA-Z0-9]", "")
-      )
-    )
-  }
-
-  private predicate rankedQuotedStringReplacements(int i, string old, string new) {
-    old = rank[i](string old2 | this.quotedStringReplacement(old2, _) | old2) and
-    this.quotedStringReplacement(old, new)
-  }
-
-  private predicate doReplaceQuotedStrings(int line, int round, string old, string new) {
-    round = 0 and
-    old = this.cmdSubstitutedLineProducer(line) and
-    new = old
-    or
-    round > 0 and
-    exists(string middle, string target, string replacement |
-      this.doReplaceQuotedStrings(line, round - 1, old, middle) and
-      this.rankedQuotedStringReplacements(round, target, replacement) and
-      new = middle.replaceAll(target, replacement)
-    )
-  }
-
-  private string quotedStringLineProducer(int i) {
-    result =
-      max(int round, string new | this.doReplaceQuotedStrings(i, round, _, new) | new order by round)
-  }
-
-  private string stmtProducer(int i) {
-    result = this.quotedStringLineProducer(i).splitAt(Bash::splitSeparator()).trim() and
-    // when splitting the line with a separator that is not present, the result is the original line which may contain other separators
-    // we only one the split parts that do not contain any of the separators
-    not result.indexOf(Bash::splitSeparator()) > -1
-  }
-
-  private predicate doStmtRestoreQuotedStrings(int line, int round, string old, string new) {
-    round = 0 and
-    old = this.stmtProducer(line) and
-    new = old
-    or
-    round > 0 and
-    exists(string middle, string target, string replacement |
-      this.doStmtRestoreQuotedStrings(line, round - 1, old, middle) and
-      this.rankedQuotedStringReplacements(round, target, replacement) and
-      new = middle.replaceAll(replacement, target)
-    )
-  }
-
-  private string restoredStmtQuotedStringLineProducer(int i) {
-    result =
-      max(int round, string new |
-        this.doStmtRestoreQuotedStrings(i, round, _, new)
-      |
-        new order by round
-      )
-  }
-
-  private predicate doStmtRestoreCmdSubstitutions(int line, int round, string old, string new) {
-    round = 0 and
-    old = this.restoredStmtQuotedStringLineProducer(line) and
-    new = old
-    or
-    round > 0 and
-    exists(string middle, string target, string replacement |
-      this.doStmtRestoreCmdSubstitutions(line, round - 1, old, middle) and
-      this.rankedCmdSubstitutionReplacements(round, target, replacement) and
-      new = middle.replaceAll(replacement, target)
-    )
-  }
-
-  string getStmt(int i) {
-    result =
-      max(int round, string new |
-        this.doStmtRestoreCmdSubstitutions(i, round, _, new)
-      |
-        new order by round
-      )
-  }
-
-  string getAStmt() { result = this.getStmt(_) }
-
-  private string cmdProducer(int i) {
-    result = this.quotedStringLineProducer(i).splitAt(Bash::separator()).trim() and
-    // when splitting the line with a separator that is not present, the result is the original line which may contain other separators
-    // we only one the split parts that do not contain any of the separators
-    not result.indexOf(Bash::separator()) > -1
-  }
-
-  private predicate doCmdRestoreQuotedStrings(int line, int round, string old, string new) {
-    round = 0 and
-    old = this.cmdProducer(line) and
-    new = old
-    or
-    round > 0 and
-    exists(string middle, string target, string replacement |
-      this.doCmdRestoreQuotedStrings(line, round - 1, old, middle) and
-      this.rankedQuotedStringReplacements(round, target, replacement) and
-      new = middle.replaceAll(replacement, target)
-    )
-  }
-
-  private string restoredCmdQuotedStringLineProducer(int i) {
-    result =
-      max(int round, string new |
-        this.doCmdRestoreQuotedStrings(i, round, _, new)
-      |
-        new order by round
-      )
-  }
-
-  private predicate doCmdRestoreCmdSubstitutions(int line, int round, string old, string new) {
-    round = 0 and
-    old = this.restoredCmdQuotedStringLineProducer(line) and
-    new = old
-    or
-    round > 0 and
-    exists(string middle, string target, string replacement |
-      this.doCmdRestoreCmdSubstitutions(line, round - 1, old, middle) and
-      this.rankedCmdSubstitutionReplacements(round, target, replacement) and
-      new = middle.replaceAll(replacement, target)
-    )
-  }
-
-  string getCmd(int i) {
-    result =
-      max(int round, string new |
-        this.doCmdRestoreCmdSubstitutions(i, round, _, new)
-      |
-        new order by round
-      )
-  }
-
-  string getACmd() { result = this.getCmd(_) }
-
-  string getCommand(int i) {
-    result = this.getCmd(i) and
-    // exclude variable declarations
-    not result.regexpMatch("^[a-zA-Z0-9\\-_]+=") and
-    // exclude the following keywords
-    not result =
-      [
-        "", "for", "in", "do", "done", "if", "then", "else", "elif", "fi", "while", "until", "case",
-        "esac", "{", "}"
-      ]
-  }
-
-  string getACommand() { result = this.getCommand(_) }
-
-  predicate getAssignment(int i, string name, string value) {
-    exists(string stmt |
-      stmt = this.getStmt(i) and
-      name = stmt.regexpCapture("^([a-zA-Z0-9\\-_]+)=.*", 1) and
-      value = stmt.regexpCapture("^[a-zA-Z0-9\\-_]+=(.*)", 1)
-    )
-  }
-
-  predicate getAnAssignment(string name, string value) { this.getAssignment(_, name, value) }
-
-  predicate getAWriteToGitHubEnv(string name, string value) {
-    exists(string raw |
-      Bash::extractFileWrite(this.getScript(), "GITHUB_ENV", raw) and
-      Bash::extractVariableAndValue(raw, name, value)
-    )
-  }
-
-  predicate getAWriteToGitHubOutput(string name, string value) {
-    exists(string raw |
-      Bash::extractFileWrite(this.getScript(), "GITHUB_OUTPUT", raw) and
-      Bash::extractVariableAndValue(raw, name, value)
-    )
-  }
-
-  predicate getAWriteToGitHubPath(string value) {
-    Bash::extractFileWrite(this.getScript(), "GITHUB_PATH", value)
-  }
-
-  predicate getAnEnvReachingGitHubOutputWrite(string var, string output_field) {
-    Bash::envReachingGitHubFileWrite(this, var, "GITHUB_OUTPUT", output_field)
-  }
-
-  predicate getACmdReachingGitHubOutputWrite(string cmd, string output_field) {
-    Bash::cmdReachingGitHubFileWrite(this, cmd, "GITHUB_OUTPUT", output_field)
-  }
-
-  predicate getAnEnvReachingGitHubEnvWrite(string var, string output_field) {
-    Bash::envReachingGitHubFileWrite(this, var, "GITHUB_ENV", output_field)
-  }
-
-  predicate getACmdReachingGitHubEnvWrite(string cmd, string output_field) {
-    Bash::cmdReachingGitHubFileWrite(this, cmd, "GITHUB_ENV", output_field)
-  }
+  ExpressionImpl getAnScriptExpr() { result.getParentNode().getNode() = script }
 }
 
 /**
diff --git a/ql/lib/codeql/actions/controlflow/internal/Cfg.qll b/ql/lib/codeql/actions/controlflow/internal/Cfg.qll
index 8a6e52309fb..5ceab79820b 100644
--- a/ql/lib/codeql/actions/controlflow/internal/Cfg.qll
+++ b/ql/lib/codeql/actions/controlflow/internal/Cfg.qll
@@ -282,7 +282,7 @@ private class RunTree extends StandardPreOrderTree instanceof Run {
         (
           child = super.getInScopeEnvVarExpr(_) or
           child = super.getAnScriptExpr() or
-          child = super.getScriptScalar()
+          child = super.getScript()
         ) and
         l = child.getLocation()
       |
diff --git a/ql/lib/codeql/actions/dataflow/FlowSources.qll b/ql/lib/codeql/actions/dataflow/FlowSources.qll
index f1fb2073ed0..b30fd5495ed 100644
--- a/ql/lib/codeql/actions/dataflow/FlowSources.qll
+++ b/ql/lib/codeql/actions/dataflow/FlowSources.qll
@@ -86,7 +86,8 @@ class GitCommandSource extends RemoteFlowSource, CommandSource {
         exists(Uses uses |
           checkout = uses and
           uses.getCallee() = "actions/checkout" and
-          exists(uses.getArgument("ref"))
+          exists(uses.getArgument("ref")) and
+          not uses.getArgument("ref").matches("%base%")
         )
         or
         checkout instanceof GitMutableRefCheckout
@@ -97,9 +98,9 @@ class GitCommandSource extends RemoteFlowSource, CommandSource {
         or
         checkout instanceof GhSHACheckout
       ) and
-      this.asExpr() = run.getScriptScalar() and
+      this.asExpr() = run.getScript() and
       checkout.getAFollowingStep() = run and
-      run.getACommand() = cmd and
+      run.getScript().getACommand() = cmd and
       cmd.indexOf("git") = 0 and
       untrustedGitCommandsDataModel(cmd_regex, flag) and
       cmd.regexpMatch(cmd_regex)
@@ -127,8 +128,8 @@ class GitHubEventPathSource extends RemoteFlowSource, CommandSource {
   // PR_TITLE=$(jq --raw-output .pull_request.title ${GITHUB_EVENT_PATH})
   // BODY=$(jq -r '.issue.body' "$GITHUB_EVENT_PATH" | sed -n '3p')
   GitHubEventPathSource() {
-    this.asExpr() = run.getScriptScalar() and
-    run.getACommand() = cmd and
+    this.asExpr() = run.getScript() and
+    run.getScript().getACommand() = cmd and
     cmd.matches("jq%") and
     cmd.matches("%GITHUB_EVENT_PATH%") and
     exists(string regexp |
@@ -207,10 +208,11 @@ private class CheckoutSource extends RemoteFlowSource, FileSource {
     // but PRHeadCheckoutStep uses Taint Tracking anc causes a non-Monolitic Recursion error
     // so we list all the subclasses of PRHeadCheckoutStep here and use actions/checkout as a workaround
     // instead of using  ActionsMutableRefCheckout and ActionsSHACheckout
-    exists(Uses u |
-      this.asExpr() = u and
-      u.getCallee() = "actions/checkout" and
-      exists(u.getArgument("ref"))
+    exists(Uses uses |
+      this.asExpr() = uses and
+      uses.getCallee() = "actions/checkout" and
+      exists(uses.getArgument("ref")) and
+      not uses.getArgument("ref").matches("%base%")
     )
     or
     this.asExpr() instanceof GitMutableRefCheckout
diff --git a/ql/lib/codeql/actions/dataflow/FlowSteps.qll b/ql/lib/codeql/actions/dataflow/FlowSteps.qll
index 787a5f72084..0f7e906685b 100644
--- a/ql/lib/codeql/actions/dataflow/FlowSteps.qll
+++ b/ql/lib/codeql/actions/dataflow/FlowSteps.qll
@@ -23,7 +23,7 @@ predicate envToOutputStoreStep(DataFlow::Node pred, DataFlow::Node succ, DataFlo
   exists(Run run, string var, string field |
     run.getInScopeEnvVarExpr(var) = pred.asExpr() and
     succ.asExpr() = run and
-    Bash::envReachingGitHubFileWrite(run, var, "GITHUB_OUTPUT", field) and
+    run.getScript().getAnEnvReachingGitHubOutputWrite(var, field) and
     c = any(DataFlow::FieldContent ct | ct.getName() = field)
   )
 }
@@ -35,8 +35,8 @@ predicate envToEnvStoreStep(DataFlow::Node pred, DataFlow::Node succ, DataFlow::
     run.getInScopeEnvVarExpr(var) = pred.asExpr() and
     // we store the taint on the enclosing job since the may not exist an implicit env attribute
     succ.asExpr() = run.getEnclosingJob() and
-    Bash::envReachingGitHubFileWrite(run, var, "GITHUB_ENV", field) and
-    c = any(DataFlow::FieldContent ct | ct.getName() = field) //and
+    run.getScript().getAnEnvReachingGitHubEnvWrite(var, field) and
+    c = any(DataFlow::FieldContent ct | ct.getName() = field)
   )
 }
 
@@ -55,12 +55,12 @@ predicate commandToOutputStoreStep(DataFlow::Node pred, DataFlow::Node succ, Dat
       or
       exists(FileSource source |
         source.asExpr().(Step).getAFollowingStep() = run and
-        Bash::outputsPartialFileContent(run, cmd)
+        run.getScript().getAFileReadCommand() = cmd
       )
     ) and
-    Bash::cmdReachingGitHubFileWrite(run, cmd, "GITHUB_OUTPUT", key) and
+    run.getScript().getACmdReachingGitHubOutputWrite(cmd, key) and
     c = any(DataFlow::FieldContent ct | ct.getName() = key) and
-    pred.asExpr() = run.getScriptScalar() and
+    pred.asExpr() = run.getScript() and
     succ.asExpr() = run
   )
 }
@@ -80,12 +80,12 @@ predicate commandToEnvStoreStep(DataFlow::Node pred, DataFlow::Node succ, DataFl
       or
       exists(FileSource source |
         source.asExpr().(Step).getAFollowingStep() = run and
-        Bash::outputsPartialFileContent(run, cmd)
+        run.getScript().getAFileReadCommand() = cmd
       )
     ) and
-    Bash::cmdReachingGitHubFileWrite(run, cmd, "GITHUB_ENV", key) and
+    run.getScript().getACmdReachingGitHubEnvWrite(cmd, key) and
     c = any(DataFlow::FieldContent ct | ct.getName() = key) and
-    pred.asExpr() = run.getScriptScalar() and
+    pred.asExpr() = run.getScript() and
     // we store the taint on the enclosing job since there may not be an implicit env attribute
     succ.asExpr() = run.getEnclosingJob()
   )
diff --git a/ql/lib/codeql/actions/dataflow/TaintSteps.qll b/ql/lib/codeql/actions/dataflow/TaintSteps.qll
index de64a0dd6f4..e9d5a44c929 100644
--- a/ql/lib/codeql/actions/dataflow/TaintSteps.qll
+++ b/ql/lib/codeql/actions/dataflow/TaintSteps.qll
@@ -22,14 +22,14 @@ class AdditionalTaintStep extends Unit {
 }
 
 /**
- * A download artifact step followed by a step that may use downloaded artifacts.
+ * A file source step followed by a Run step may read the file.
  */
 predicate fileDownloadToRunStep(DataFlow::Node pred, DataFlow::Node succ) {
   exists(FileSource source, Run run |
     pred = source and
     source.asExpr().(Step).getAFollowingStep() = run and
-    succ.asExpr() = run.getScriptScalar() and
-    Bash::outputsPartialFileContent(run, run.getACommand())
+    succ.asExpr() = run.getScript() and
+    exists(run.getScript().getAFileReadCommand())
   )
 }
 
diff --git a/ql/lib/codeql/actions/security/ArgumentInjectionQuery.qll b/ql/lib/codeql/actions/security/ArgumentInjectionQuery.qll
index 18ff398ebab..a0309437292 100644
--- a/ql/lib/codeql/actions/security/ArgumentInjectionQuery.qll
+++ b/ql/lib/codeql/actions/security/ArgumentInjectionQuery.qll
@@ -17,11 +17,11 @@ abstract class ArgumentInjectionSink extends DataFlow::Node {
 bindingset[var]
 predicate envToArgInjSink(string var, Run run, string command) {
   exists(string argument, string cmd, string regexp, int command_group, int argument_group |
-    run.getACommand() = cmd and
+    run.getScript().getACommand() = cmd and
     argumentInjectionSinksDataModel(regexp, command_group, argument_group) and
     command = cmd.regexpCapture(regexp, command_group) and
     argument = cmd.regexpCapture(regexp, argument_group) and
-    Bash::envReachingRunExpr(run, var, argument) and
+    Bash::envReachingRunExpr(run.getScript(), var, argument) and
     exists(run.getInScopeEnvVarExpr(var))
   )
 }
@@ -40,15 +40,15 @@ class ArgumentInjectionFromEnvVarSink extends ArgumentInjectionSink {
   ArgumentInjectionFromEnvVarSink() {
     exists(Run run, string var |
       envToArgInjSink(var, run, command) and
-      run.getScriptScalar() = this.asExpr() and
+      run.getScript() = this.asExpr() and
       exists(run.getInScopeEnvVarExpr(var))
     )
     or
     exists(
       Run run, string cmd, string argument, string regexp, int argument_group, int command_group
     |
-      run.getACommand() = cmd and
-      run.getScriptScalar() = this.asExpr() and
+      run.getScript().getACommand() = cmd and
+      run.getScript() = this.asExpr() and
       argumentInjectionSinksDataModel(regexp, command_group, argument_group) and
       argument = cmd.regexpCapture(regexp, argument_group) and
       command = cmd.regexpCapture(regexp, command_group) and
@@ -75,8 +75,8 @@ class ArgumentInjectionFromCommandSink extends ArgumentInjectionSink {
       int command_group
     |
       run = source.getEnclosingRun() and
-      this.asExpr() = run.getScriptScalar() and
-      cmd = run.getACommand() and
+      this.asExpr() = run.getScript() and
+      cmd = run.getScript().getACommand() and
       argumentInjectionSinksDataModel(regexp, command_group, argument_group) and
       argument = cmd.regexpCapture(regexp, argument_group) and
       command = cmd.regexpCapture(regexp, command_group)
@@ -106,8 +106,8 @@ private module ArgumentInjectionConfig implements DataFlow::ConfigSig {
     exists(
       Run run, string argument, string cmd, string regexp, int command_group, int argument_group
     |
-      run.getScriptScalar() = source.asExpr() and
-      run.getACommand() = cmd and
+      run.getScript() = source.asExpr() and
+      run.getScript().getACommand() = cmd and
       argumentInjectionSinksDataModel(regexp, command_group, argument_group) and
       argument = cmd.regexpCapture(regexp, argument_group) and
       argument.regexpMatch(".*\\$(\\{)?(GITHUB_HEAD_REF).*")
@@ -119,7 +119,7 @@ private module ArgumentInjectionConfig implements DataFlow::ConfigSig {
   predicate isAdditionalFlowStep(DataFlow::Node pred, DataFlow::Node succ) {
     exists(Run run, string var |
       run.getInScopeEnvVarExpr(var) = pred.asExpr() and
-      succ.asExpr() = run.getScriptScalar() and
+      succ.asExpr() = run.getScript() and
       envToArgInjSink(var, run, _)
     )
   }
diff --git a/ql/lib/codeql/actions/security/ArtifactPoisoningQuery.qll b/ql/lib/codeql/actions/security/ArtifactPoisoningQuery.qll
index 31a9edd03b3..d06b125ca32 100644
--- a/ql/lib/codeql/actions/security/ArtifactPoisoningQuery.qll
+++ b/ql/lib/codeql/actions/security/ArtifactPoisoningQuery.qll
@@ -155,15 +155,21 @@ class ActionsGitHubScriptDownloadStep extends UntrustedArtifactDownloadStep, Use
   }
 
   override string getPath() {
-    if this.getAFollowingStep().(Run).getACommand().regexpMatch(unzipRegexp() + unzipDirArgRegexp())
+    if
+      this.getAFollowingStep()
+          .(Run)
+          .getScript()
+          .getACommand()
+          .regexpMatch(unzipRegexp() + unzipDirArgRegexp())
     then
       result =
         normalizePath(trimQuotes(this.getAFollowingStep()
                 .(Run)
+                .getScript()
                 .getACommand()
                 .regexpCapture(unzipRegexp() + unzipDirArgRegexp(), 2)))
     else
-      if this.getAFollowingStep().(Run).getACommand().regexpMatch(unzipRegexp())
+      if this.getAFollowingStep().(Run).getScript().getACommand().regexpMatch(unzipRegexp())
       then result = "GITHUB_WORKSPACE/"
       else none()
   }
@@ -172,31 +178,37 @@ class ActionsGitHubScriptDownloadStep extends UntrustedArtifactDownloadStep, Use
 class GHRunArtifactDownloadStep extends UntrustedArtifactDownloadStep, Run {
   GHRunArtifactDownloadStep() {
     // eg: - run: gh run download ${{ github.event.workflow_run.id }} --repo "${GITHUB_REPOSITORY}" --name "artifact_name"
-    this.getACommand().regexpMatch(".*gh\\s+run\\s+download.*") and
-    this.getACommand().matches("%github.event.workflow_run.id%") and
+    this.getScript().getACommand().regexpMatch(".*gh\\s+run\\s+download.*") and
+    this.getScript().getACommand().matches("%github.event.workflow_run.id%") and
     (
-      this.getACommand().regexpMatch(unzipRegexp()) or
-      this.getAFollowingStep().(Run).getACommand().regexpMatch(unzipRegexp())
+      this.getScript().getACommand().regexpMatch(unzipRegexp()) or
+      this.getAFollowingStep().(Run).getScript().getACommand().regexpMatch(unzipRegexp())
     )
   }
 
   override string getPath() {
     if
-      this.getAFollowingStep().(Run).getACommand().regexpMatch(unzipRegexp() + unzipDirArgRegexp()) or
-      this.getACommand().regexpMatch(unzipRegexp() + unzipDirArgRegexp())
+      this.getAFollowingStep()
+          .(Run)
+          .getScript()
+          .getACommand()
+          .regexpMatch(unzipRegexp() + unzipDirArgRegexp()) or
+      this.getScript().getACommand().regexpMatch(unzipRegexp() + unzipDirArgRegexp())
     then
       result =
-        normalizePath(trimQuotes(this.getACommand()
+        normalizePath(trimQuotes(this.getScript()
+                .getACommand()
                 .regexpCapture(unzipRegexp() + unzipDirArgRegexp(), 2))) or
       result =
         normalizePath(trimQuotes(this.getAFollowingStep()
                 .(Run)
+                .getScript()
                 .getACommand()
                 .regexpCapture(unzipRegexp() + unzipDirArgRegexp(), 2)))
     else
       if
-        this.getAFollowingStep().(Run).getACommand().regexpMatch(unzipRegexp()) or
-        this.getACommand().regexpMatch(unzipRegexp())
+        this.getAFollowingStep().(Run).getScript().getACommand().regexpMatch(unzipRegexp()) or
+        this.getScript().getACommand().regexpMatch(unzipRegexp())
       then result = "GITHUB_WORKSPACE/"
       else none()
   }
@@ -213,24 +225,30 @@ class DirectArtifactDownloadStep extends UntrustedArtifactDownloadStep, Run {
     //     gh api $url > "$name.zip"
     //     unzip -d "$name" "$name.zip"
     //   done
-    this.getACommand().matches("%github.event.workflow_run.artifacts_url%") and
+    this.getScript().getACommand().matches("%github.event.workflow_run.artifacts_url%") and
     (
-      this.getACommand().regexpMatch(unzipRegexp()) or
-      this.getAFollowingStep().(Run).getACommand().regexpMatch(unzipRegexp())
+      this.getScript().getACommand().regexpMatch(unzipRegexp()) or
+      this.getAFollowingStep().(Run).getScript().getACommand().regexpMatch(unzipRegexp())
     )
   }
 
   override string getPath() {
     if
-      this.getACommand().regexpMatch(unzipRegexp() + unzipDirArgRegexp()) or
-      this.getAFollowingStep().(Run).getACommand().regexpMatch(unzipRegexp() + unzipDirArgRegexp())
+      this.getScript().getACommand().regexpMatch(unzipRegexp() + unzipDirArgRegexp()) or
+      this.getAFollowingStep()
+          .(Run)
+          .getScript()
+          .getACommand()
+          .regexpMatch(unzipRegexp() + unzipDirArgRegexp())
     then
       result =
-        normalizePath(trimQuotes(this.getACommand()
+        normalizePath(trimQuotes(this.getScript()
+                .getACommand()
                 .regexpCapture(unzipRegexp() + unzipDirArgRegexp(), 2))) or
       result =
         normalizePath(trimQuotes(this.getAFollowingStep()
                 .(Run)
+                .getScript()
                 .getACommand()
                 .regexpCapture(unzipRegexp() + unzipDirArgRegexp(), 2)))
     else result = "GITHUB_WORKSPACE/"
@@ -246,7 +264,7 @@ class ArtifactPoisoningSink extends DataFlow::Node {
     // excluding artifacts downloaded to /tmp
     not download.getPath().regexpMatch("^/tmp.*") and
     (
-      poisonable.(Run).getScriptScalar() = this.asExpr() and
+      poisonable.(Run).getScript() = this.asExpr() and
       (
         // Check if the poisonable step is a local script execution step
         // and the path of the command or script matches the path of the downloaded artifact
@@ -280,7 +298,7 @@ private module ArtifactPoisoningConfig implements DataFlow::ConfigSig {
       pred instanceof ArtifactSource and
       pred.asExpr().(Step).getAFollowingStep() = step and
       (
-        succ.asExpr() = step.(Run).getScriptScalar() or
+        succ.asExpr() = step.(Run).getScript() or
         succ.asExpr() = step.(UsesStep)
       )
     )
@@ -288,8 +306,8 @@ private module ArtifactPoisoningConfig implements DataFlow::ConfigSig {
     exists(Run run |
       pred instanceof ArtifactSource and
       pred.asExpr().(Step).getAFollowingStep() = run and
-      succ.asExpr() = run.getScriptScalar() and
-      Bash::outputsPartialFileContent(run, run.getACommand())
+      succ.asExpr() = run.getScript() and
+      exists(run.getScript().getAFileReadCommand())
     )
   }
 }
diff --git a/ql/lib/codeql/actions/security/CodeInjectionQuery.qll b/ql/lib/codeql/actions/security/CodeInjectionQuery.qll
index ca72fe00d16..fac498f72da 100644
--- a/ql/lib/codeql/actions/security/CodeInjectionQuery.qll
+++ b/ql/lib/codeql/actions/security/CodeInjectionQuery.qll
@@ -31,8 +31,8 @@ private module CodeInjectionConfig implements DataFlow::ConfigSig {
     exists(Run run |
       pred instanceof FileSource and
       pred.asExpr().(Step).getAFollowingStep() = run and
-      succ.asExpr() = run.getScriptScalar() and
-      Bash::outputsPartialFileContent(run, run.getACommand())
+      succ.asExpr() = run.getScript() and
+      exists(run.getScript().getAFileReadCommand())
     )
   }
 }
diff --git a/ql/lib/codeql/actions/security/ControlChecks.qll b/ql/lib/codeql/actions/security/ControlChecks.qll
index 86de44c3b5c..86c7d989522 100644
--- a/ql/lib/codeql/actions/security/ControlChecks.qll
+++ b/ql/lib/codeql/actions/security/ControlChecks.qll
@@ -283,8 +283,8 @@ class BashCommentVsHeadDateCheck extends CommentVsHeadDateCheck, Run {
   BashCommentVsHeadDateCheck() {
     // eg: if [[ $(date -d "$pushed_at" +%s) -gt $(date -d "$COMMENT_AT" +%s) ]]; then
     exists(string cmd1, string cmd2 |
-      cmd1 = this.getACommand() and
-      cmd2 = this.getACommand() and
+      cmd1 = this.getScript().getACommand() and
+      cmd2 = this.getScript().getACommand() and
       not cmd1 = cmd2 and
       cmd1.toLowerCase().regexpMatch("date\\s+-d.*(commit|pushed|comment|commented)_at.*") and
       cmd2.toLowerCase().regexpMatch("date\\s+-d.*(commit|pushed|comment|commented)_at.*")
diff --git a/ql/lib/codeql/actions/security/EnvPathInjectionQuery.qll b/ql/lib/codeql/actions/security/EnvPathInjectionQuery.qll
index 1f53c938436..859f625e068 100644
--- a/ql/lib/codeql/actions/security/EnvPathInjectionQuery.qll
+++ b/ql/lib/codeql/actions/security/EnvPathInjectionQuery.qll
@@ -25,15 +25,15 @@ class EnvPathInjectionFromFileReadSink extends EnvPathInjectionSink {
         step instanceof UntrustedArtifactDownloadStep or
         step instanceof PRHeadCheckoutStep
       ) and
-      this.asExpr() = run.getScriptScalar() and
+      this.asExpr() = run.getScript() and
       step.getAFollowingStep() = run and
       (
         exists(string cmd |
-          Bash::cmdReachingGitHubFileWrite(run, cmd, "GITHUB_PATH", _) and
-          Bash::outputsPartialFileContent(run, cmd)
+          run.getScript().getACmdReachingGitHubPathWrite(cmd) and
+          run.getScript().getAFileReadCommand() = cmd
         )
         or
-        Bash::fileToGitHubPath(run, _)
+        run.getScript().fileToGitHubPath(_)
       )
     )
   }
@@ -49,9 +49,8 @@ class EnvPathInjectionFromFileReadSink extends EnvPathInjectionSink {
 class EnvPathInjectionFromCommandSink extends EnvPathInjectionSink {
   EnvPathInjectionFromCommandSink() {
     exists(CommandSource source |
-      this.asExpr() = source.getEnclosingRun().getScriptScalar() and
-      Bash::cmdReachingGitHubFileWrite(source.getEnclosingRun(), source.getCommand(), "GITHUB_PATH",
-        _)
+      this.asExpr() = source.getEnclosingRun().getScript() and
+      source.getEnclosingRun().getScript().getACmdReachingGitHubPathWrite(source.getCommand())
     )
   }
 }
@@ -67,9 +66,9 @@ class EnvPathInjectionFromCommandSink extends EnvPathInjectionSink {
 class EnvPathInjectionFromEnvVarSink extends EnvPathInjectionSink {
   EnvPathInjectionFromEnvVarSink() {
     exists(Run run, string var_name |
-      Bash::envReachingGitHubFileWrite(run, var_name, "GITHUB_PATH", _) and
+      run.getScript().getAnEnvReachingGitHubPathWrite(var_name) and
       exists(run.getInScopeEnvVarExpr(var_name)) and
-      run.getScriptScalar() = this.asExpr()
+      run.getScript() = this.asExpr()
     )
   }
 }
@@ -90,8 +89,12 @@ private module EnvPathInjectionConfig implements DataFlow::ConfigSig {
   predicate isAdditionalFlowStep(DataFlow::Node pred, DataFlow::Node succ) {
     exists(Run run, string var |
       run.getInScopeEnvVarExpr(var) = pred.asExpr() and
-      succ.asExpr() = run.getScriptScalar() and
-      Bash::envReachingGitHubFileWrite(run, var, ["GITHUB_ENV", "GITHUB_OUTPUT", "GITHUB_PATH"], _)
+      succ.asExpr() = run.getScript() and
+      (
+        run.getScript().getAnEnvReachingGitHubOutputWrite(var, _) or
+        run.getScript().getAnEnvReachingGitHubEnvWrite(var, _) or
+        run.getScript().getAnEnvReachingGitHubPathWrite(var)
+      )
     )
     or
     exists(Uses step |
@@ -104,8 +107,8 @@ private module EnvPathInjectionConfig implements DataFlow::ConfigSig {
     exists(Run run |
       pred instanceof FileSource and
       pred.asExpr().(Step).getAFollowingStep() = run and
-      succ.asExpr() = run.getScriptScalar() and
-      Bash::outputsPartialFileContent(run, run.getACommand())
+      succ.asExpr() = run.getScript() and
+      exists(run.getScript().getAFileReadCommand())
     )
   }
 }
diff --git a/ql/lib/codeql/actions/security/EnvVarInjectionQuery.qll b/ql/lib/codeql/actions/security/EnvVarInjectionQuery.qll
index dd6b8342185..214e97fed6b 100644
--- a/ql/lib/codeql/actions/security/EnvVarInjectionQuery.qll
+++ b/ql/lib/codeql/actions/security/EnvVarInjectionQuery.qll
@@ -28,15 +28,15 @@ class EnvVarInjectionFromFileReadSink extends EnvVarInjectionSink {
         step instanceof UntrustedArtifactDownloadStep or
         step instanceof PRHeadCheckoutStep
       ) and
-      this.asExpr() = run.getScriptScalar() and
+      this.asExpr() = run.getScript() and
       step.getAFollowingStep() = run and
       (
         exists(string cmd |
-          Bash::cmdReachingGitHubFileWrite(run, cmd, "GITHUB_ENV", _) and
-          Bash::outputsPartialFileContent(run, cmd)
+          run.getScript().getACmdReachingGitHubEnvWrite(cmd, _) and
+          run.getScript().getAFileReadCommand() = cmd
         )
         or
-        Bash::fileToGitHubEnv(run, _)
+        run.getScript().fileToGitHubEnv(_)
       )
     )
   }
@@ -52,9 +52,8 @@ class EnvVarInjectionFromFileReadSink extends EnvVarInjectionSink {
 class EnvVarInjectionFromCommandSink extends EnvVarInjectionSink {
   EnvVarInjectionFromCommandSink() {
     exists(CommandSource source |
-      this.asExpr() = source.getEnclosingRun().getScriptScalar() and
-      Bash::cmdReachingGitHubFileWrite(source.getEnclosingRun(), source.getCommand(), "GITHUB_ENV",
-        _)
+      this.asExpr() = source.getEnclosingRun().getScript() and
+      source.getEnclosingRun().getScript().getACmdReachingGitHubEnvWrite(source.getCommand(), _)
     )
   }
 }
@@ -71,8 +70,8 @@ class EnvVarInjectionFromEnvVarSink extends EnvVarInjectionSink {
   EnvVarInjectionFromEnvVarSink() {
     exists(Run run, string var_name |
       exists(run.getInScopeEnvVarExpr(var_name)) and
-      run.getScriptScalar() = this.asExpr() and
-      Bash::envReachingGitHubFileWrite(run, var_name, "GITHUB_ENV", _)
+      run.getScript() = this.asExpr() and
+      run.getScript().getAnEnvReachingGitHubEnvWrite(var_name, _)
     )
   }
 }
@@ -109,8 +108,12 @@ private module EnvVarInjectionConfig implements DataFlow::ConfigSig {
   predicate isAdditionalFlowStep(DataFlow::Node pred, DataFlow::Node succ) {
     exists(Run run, string var |
       run.getInScopeEnvVarExpr(var) = pred.asExpr() and
-      succ.asExpr() = run.getScriptScalar() and
-      Bash::envReachingGitHubFileWrite(run, var, ["GITHUB_ENV", "GITHUB_OUTPUT", "GITHUB_PATH"], _)
+      succ.asExpr() = run.getScript() and
+      (
+        run.getScript().getAnEnvReachingGitHubEnvWrite(var, _)
+        or
+        run.getScript().getAnEnvReachingGitHubOutputWrite(var, _)
+      )
     )
     or
     exists(Uses step |
@@ -123,8 +126,8 @@ private module EnvVarInjectionConfig implements DataFlow::ConfigSig {
     exists(Run run |
       pred instanceof FileSource and
       pred.asExpr().(Step).getAFollowingStep() = run and
-      succ.asExpr() = run.getScriptScalar() and
-      Bash::outputsPartialFileContent(run, run.getACommand())
+      succ.asExpr() = run.getScript() and
+      exists(run.getScript().getAFileReadCommand())
     )
   }
 }
diff --git a/ql/lib/codeql/actions/security/OutputClobberingQuery.qll b/ql/lib/codeql/actions/security/OutputClobberingQuery.qll
index 4f9eeef7579..e959c7d60ca 100644
--- a/ql/lib/codeql/actions/security/OutputClobberingQuery.qll
+++ b/ql/lib/codeql/actions/security/OutputClobberingQuery.qll
@@ -19,7 +19,7 @@ abstract class OutputClobberingSink extends DataFlow::Node { }
  */
 class OutputClobberingFromFileReadSink extends OutputClobberingSink {
   OutputClobberingFromFileReadSink() {
-    exists(Run run, Step step |
+    exists(Run run, Step step, string field1, string field2 |
       (
         step instanceof UntrustedArtifactDownloadStep
         or
@@ -31,7 +31,8 @@ class OutputClobberingFromFileReadSink extends OutputClobberingSink {
         exists(Uses uses |
           step = uses and
           uses.getCallee() = "actions/checkout" and
-          exists(uses.getArgument("ref"))
+          exists(uses.getArgument("ref")) and
+          not uses.getArgument("ref").matches("%base%")
         )
         or
         step instanceof GitMutableRefCheckout
@@ -43,14 +44,28 @@ class OutputClobberingFromFileReadSink extends OutputClobberingSink {
         step instanceof GhSHACheckout
       ) and
       step.getAFollowingStep() = run and
-      this.asExpr() = run.getScriptScalar() and
+      this.asExpr() = run.getScript() and
+      // A write to GITHUB_OUTPUT that is not attacker-controlled
+      exists(string str |
+        // The output of a command that is not a file read command
+        run.getScript().getACmdReachingGitHubOutputWrite(str, field1) and
+        not str = run.getScript().getAFileReadCommand()
+        or
+        // A hard-coded string
+        run.getScript().getAWriteToGitHubOutput(field1, str) and
+        str.regexpMatch("[\"'0-9a-zA-Z_\\-]+")
+      ) and
+      // A write to GITHUB_OUTPUT that is attacker-controlled
       (
+        // echo "sha=$(<test-results/sha-number)" >> $GITHUB_OUTPUT
         exists(string cmd |
-          Bash::cmdReachingGitHubFileWrite(run, cmd, "GITHUB_OUTPUT", _) and
-          Bash::outputsPartialFileContent(run, cmd)
+          run.getScript().getACmdReachingGitHubOutputWrite(cmd, field2) and
+          run.getScript().getAFileReadCommand() = cmd
         )
         or
-        Bash::fileToGitHubOutput(run, _)
+        // cat test-results/.vars >> $GITHUB_OUTPUT
+        run.getScript().fileToGitHubOutput(_) and
+        field2 = "UNKNOWN"
       )
     )
   }
@@ -66,16 +81,24 @@ class OutputClobberingFromFileReadSink extends OutputClobberingSink {
  */
 class OutputClobberingFromEnvVarSink extends OutputClobberingSink {
   OutputClobberingFromEnvVarSink() {
-    exists(Run run, string var, string field |
-      Bash::envReachingGitHubFileWrite(run, var, "GITHUB_OUTPUT", field) and
-      // there is a different output variable in the same script
-      // TODO: key2/value2 should be declared before key/value
-      exists(string field2 |
-        run.getAWriteToGitHubOutput(field2, _) and
-        not field2 = field
+    exists(Run run, string field1, string field2 |
+      // A write to GITHUB_OUTPUT that is attacker-controlled
+      exists(string var |
+        run.getScript().getAnEnvReachingGitHubOutputWrite(var, field1) and
+        exists(run.getInScopeEnvVarExpr(var)) and
+        run.getScript() = this.asExpr()
       ) and
-      exists(run.getInScopeEnvVarExpr(var)) and
-      run.getScriptScalar() = this.asExpr()
+      // A write to GITHUB_OUTPUT that is not attacker-controlled
+      exists(string str |
+        // The output of a command that is not a file read command
+        run.getScript().getACmdReachingGitHubOutputWrite(str, field2) and
+        not str = run.getScript().getAFileReadCommand()
+        or
+        // A hard-coded string
+        run.getScript().getAWriteToGitHubOutput(field2, str) and
+        str.regexpMatch("[\"'0-9a-zA-Z_\\-]+")
+      ) and
+      not field2 = field1
     )
   }
 }
@@ -97,13 +120,18 @@ class OutputClobberingFromEnvVarSink extends OutputClobberingSink {
  *          echo $BODY
  */
 class WorkflowCommandClobberingFromEnvVarSink extends OutputClobberingSink {
+  string clobbering_var;
+  string clobbered_value;
+
   WorkflowCommandClobberingFromEnvVarSink() {
-    exists(Run run, string clobbering_line, string var_name |
-      Bash::singleLineWorkflowCmd(run.getACommand(), "set-output", _, _) and
-      run.getACommand() = clobbering_line and
-      clobbering_line.regexpMatch(".*echo\\s+(-e\\s+)?(\"|')?\\$(\\{)?" + var_name + ".*") and
-      exists(run.getInScopeEnvVarExpr(var_name)) and
-      run.getScriptScalar() = this.asExpr()
+    exists(Run run, string workflow_cmd_stmt, string clobbering_stmt |
+      run.getScript() = this.asExpr() and
+      run.getScript().getAStmt() = clobbering_stmt and
+      clobbering_stmt.regexpMatch("echo\\s+(-e\\s+)?(\"|')?\\$(\\{)?" + clobbering_var + ".*") and
+      exists(run.getInScopeEnvVarExpr(clobbering_var)) and
+      run.getScript().getAStmt() = workflow_cmd_stmt and
+      clobbered_value =
+        trimQuotes(workflow_cmd_stmt.regexpCapture(".*::set-output\\s+name=.*::(.*)", 1))
     )
   }
 }
@@ -133,30 +161,35 @@ class WorkflowCommandClobberingFromEnvVarSink extends OutputClobberingSink {
  *          echo "::set-output name=OUTPUT::SAFE"
  */
 class WorkflowCommandClobberingFromFileReadSink extends OutputClobberingSink {
+  string clobbering_cmd;
+
   WorkflowCommandClobberingFromFileReadSink() {
-    exists(Run run, string clobbering_line |
-      run.getScriptScalar() = this.asExpr() and
-      Bash::singleLineWorkflowCmd(run.getACommand(), "set-output", _, _) and
-      run.getACommand() = clobbering_line and
+    exists(Run run, string clobbering_stmt |
+      run.getScript() = this.asExpr() and
+      run.getScript().getAStmt() = clobbering_stmt and
       (
-        // A file is read and its content is assigned to an env var that gets printed to stdout
+        // A file's content is assigned to an env var that gets printed to stdout
         // - run: |
         //     foo=$(<pr-id.txt)"
         //     echo "${foo}"
-        exists(string var_name, string value |
-          run.getAnAssignment(var_name, value) and
-          Bash::outputsPartialFileContent(run, trimQuotes(value)) and
-          clobbering_line.regexpMatch(".*echo\\s+(-e\\s+)?(\"|')?\\$(\\{)?" + var_name + ".*")
+        exists(string var, string value |
+          run.getScript().getAnAssignment(var, value) and
+          clobbering_cmd = run.getScript().getAFileReadCommand() and
+          trimQuotes(value) = ["$(" + clobbering_cmd + ")", "`" + clobbering_cmd + "`"] and
+          clobbering_stmt.regexpMatch("echo.*\\$(\\{)?" + var + ".*")
         )
         or
         // A file is read and its content is printed to stdout
-        // - run: echo "foo=$(<pr-id.txt)"
-        clobbering_line.regexpMatch(".*echo\\s+(-e)?\\s*(\"|')?") and
-        clobbering_line.regexpMatch(["ls", Bash::partialFileContentCommand()] + "\\s.*")
-        or
-        // A file content is printed to stdout
-        // - run: cat pr-id.txt
-        clobbering_line.regexpMatch(["ls", Bash::partialFileContentCommand()] + "\\s.*")
+        clobbering_cmd = run.getScript().getACommand() and
+        clobbering_cmd.regexpMatch(["ls", Bash::fileReadCommand()] + "\\s.*") and
+        (
+          // - run: echo "foo=$(<pr-id.txt)"
+          clobbering_stmt.regexpMatch("echo.*" + clobbering_cmd + ".*")
+          or
+          // A file content is printed to stdout
+          // - run: cat pr-id.txt
+          clobbering_stmt.indexOf(clobbering_cmd) = 0
+        )
       )
     )
   }
@@ -181,8 +214,8 @@ private module OutputClobberingConfig implements DataFlow::ConfigSig {
   predicate isAdditionalFlowStep(DataFlow::Node pred, DataFlow::Node succ) {
     exists(Run run, string var |
       run.getInScopeEnvVarExpr(var) = pred.asExpr() and
-      succ.asExpr() = run.getScriptScalar() and
-      run.getAWriteToGitHubOutput(_, _)
+      succ.asExpr() = run.getScript() and
+      run.getScript().getAWriteToGitHubOutput(_, _)
     )
     or
     exists(Uses step |
@@ -195,10 +228,10 @@ private module OutputClobberingConfig implements DataFlow::ConfigSig {
     exists(Run run |
       pred instanceof FileSource and
       pred.asExpr().(Step).getAFollowingStep() = run and
-      succ.asExpr() = run.getScriptScalar() and
+      succ.asExpr() = run.getScript() and
       (
-        Bash::outputsPartialFileContent(run, run.getACommand()) or
-        Bash::singleLineWorkflowCmd(run.getACommand(), "set-output", _, _)
+        exists(run.getScript().getAFileReadCommand()) or
+        run.getScript().getAStmt().matches("%::set-output %")
       )
     )
   }
diff --git a/ql/lib/codeql/actions/security/PoisonableSteps.qll b/ql/lib/codeql/actions/security/PoisonableSteps.qll
index 5e8731010ca..85932181aed 100644
--- a/ql/lib/codeql/actions/security/PoisonableSteps.qll
+++ b/ql/lib/codeql/actions/security/PoisonableSteps.qll
@@ -18,7 +18,7 @@ class PoisonableCommandStep extends PoisonableStep, Run {
   PoisonableCommandStep() {
     exists(string regexp |
       poisonableCommandsDataModel(regexp) and
-      this.getACommand().regexpMatch("^" + regexp + ".*")
+      this.getScript().getACommand().regexpMatch("^" + regexp + ".*")
     )
   }
 }
@@ -46,7 +46,7 @@ class LocalScriptExecutionRunStep extends PoisonableStep, Run {
   string path;
 
   LocalScriptExecutionRunStep() {
-    exists(string cmd, string regexp, int path_group | cmd = this.getACommand() |
+    exists(string cmd, string regexp, int path_group | cmd = this.getScript().getACommand() |
       poisonableLocalScriptsDataModel(regexp, path_group) and
       path = cmd.regexpCapture(regexp, path_group)
     )
@@ -58,12 +58,3 @@ class LocalScriptExecutionRunStep extends PoisonableStep, Run {
 class LocalActionUsesStep extends PoisonableStep, UsesStep {
   LocalActionUsesStep() { this.getCallee().matches("./%") }
 }
-
-class EnvVarInjectionFromFileReadRunStep extends PoisonableStep, Run {
-  string value;
-
-  EnvVarInjectionFromFileReadRunStep() {
-    this.getAWriteToGitHubEnv(_, value) and
-    Bash::outputsPartialFileContent(this, value)
-  }
-}
diff --git a/ql/lib/codeql/actions/security/UntrustedCheckoutQuery.qll b/ql/lib/codeql/actions/security/UntrustedCheckoutQuery.qll
index 28ee12d47cf..e9bf1edfe7d 100644
--- a/ql/lib/codeql/actions/security/UntrustedCheckoutQuery.qll
+++ b/ql/lib/codeql/actions/security/UntrustedCheckoutQuery.qll
@@ -61,8 +61,8 @@ private module ActionsMutableRefCheckoutConfig implements DataFlow::ConfigSig {
     exists(Run run |
       pred instanceof FileSource and
       pred.asExpr().(Step).getAFollowingStep() = run and
-      succ.asExpr() = run.getScriptScalar() and
-      Bash::outputsPartialFileContent(run, run.getACommand())
+      succ.asExpr() = run.getScript() and
+      exists(run.getScript().getAFileReadCommand())
     )
   }
 }
@@ -107,8 +107,8 @@ private module ActionsSHACheckoutConfig implements DataFlow::ConfigSig {
     exists(Run run |
       pred instanceof FileSource and
       pred.asExpr().(Step).getAFollowingStep() = run and
-      succ.asExpr() = run.getScriptScalar() and
-      Bash::outputsPartialFileContent(run, run.getACommand())
+      succ.asExpr() = run.getScript() and
+      exists(run.getScript().getAFileReadCommand())
     )
   }
 }
@@ -283,7 +283,7 @@ class ActionsSHACheckout extends SHACheckoutStep instanceof UsesStep {
 /** Checkout of a Pull Request HEAD ref using git within a Run step */
 class GitMutableRefCheckout extends MutableRefCheckoutStep instanceof Run {
   GitMutableRefCheckout() {
-    exists(string cmd | this.getACommand() = cmd |
+    exists(string cmd | this.getScript().getACommand() = cmd |
       cmd.regexpMatch("git\\s+(fetch|pull).*") and
       (
         (containsHeadRef(cmd) or containsPullRequestNumber(cmd))
@@ -306,7 +306,7 @@ class GitMutableRefCheckout extends MutableRefCheckoutStep instanceof Run {
 /** Checkout of a Pull Request HEAD ref using git within a Run step */
 class GitSHACheckout extends SHACheckoutStep instanceof Run {
   GitSHACheckout() {
-    exists(string cmd | this.getACommand() = cmd |
+    exists(string cmd | this.getScript().getACommand() = cmd |
       cmd.regexpMatch("git\\s+(fetch|pull).*") and
       (
         containsHeadSHA(cmd)
@@ -326,7 +326,7 @@ class GitSHACheckout extends SHACheckoutStep instanceof Run {
 /** Checkout of a Pull Request HEAD ref using gh within a Run step */
 class GhMutableRefCheckout extends MutableRefCheckoutStep instanceof Run {
   GhMutableRefCheckout() {
-    exists(string cmd | this.getACommand() = cmd |
+    exists(string cmd | this.getScript().getACommand() = cmd |
       cmd.regexpMatch(".*(gh|hub)\\s+pr\\s+checkout.*") and
       (
         (containsHeadRef(cmd) or containsPullRequestNumber(cmd))
@@ -348,7 +348,7 @@ class GhMutableRefCheckout extends MutableRefCheckoutStep instanceof Run {
 /** Checkout of a Pull Request HEAD ref using gh within a Run step */
 class GhSHACheckout extends SHACheckoutStep instanceof Run {
   GhSHACheckout() {
-    exists(string cmd | this.getACommand() = cmd |
+    exists(string cmd | this.getScript().getACommand() = cmd |
       cmd.regexpMatch("gh\\s+pr\\s+checkout.*") and
       (
         containsHeadSHA(cmd)
diff --git a/ql/test/library-tests/.github/workflows/commands.yml b/ql/test/library-tests/.github/workflows/commands.yml
index 11ef1a60d31..48aa5b5810b 100644
--- a/ql/test/library-tests/.github/workflows/commands.yml
+++ b/ql/test/library-tests/.github/workflows/commands.yml
@@ -1,10 +1,19 @@
 on: push
 
+defaults:
+  run:
+    shell: bash -wkf
+
 jobs:
   local_commands:
     runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -job
     steps:
-      - run: |
+
+      - shell: bash -step
+        run: |
           command1 ; command2
       - run: |
           command3 | command4
@@ -19,3 +28,12 @@ jobs:
       - run: |
           command13 "`command14` $(date | wc -l)"
 
+  local_commands2:
+    runs-on: ubuntu-latest
+    steps:
+      - shell: bash -step
+        run: |
+          command1 ; command2
+      - shell: pwsh
+        run: |
+          command3 | command4
diff --git a/ql/test/library-tests/commands.expected b/ql/test/library-tests/commands.expected
index ec19a6c79f0..e78f152e60b 100644
--- a/ql/test/library-tests/commands.expected
+++ b/ql/test/library-tests/commands.expected
@@ -1,19 +1,21 @@
-| .github/workflows/commands.yml:7:9:9:6 | Run Step | command1 |
-| .github/workflows/commands.yml:7:9:9:6 | Run Step | command2 |
-| .github/workflows/commands.yml:9:9:11:6 | Run Step | command3 |
-| .github/workflows/commands.yml:9:9:11:6 | Run Step | command4 |
-| .github/workflows/commands.yml:11:9:13:6 | Run Step | command5 "$(command6)" |
-| .github/workflows/commands.yml:11:9:13:6 | Run Step | command6 |
-| .github/workflows/commands.yml:13:9:15:6 | Run Step | command7 |
-| .github/workflows/commands.yml:13:9:15:6 | Run Step | command8 |
-| .github/workflows/commands.yml:15:9:17:6 | Run Step | command9 |
-| .github/workflows/commands.yml:15:9:17:6 | Run Step | command10 |
-| .github/workflows/commands.yml:17:9:19:6 | Run Step | command11 "`command12`" |
-| .github/workflows/commands.yml:17:9:19:6 | Run Step | command12 |
-| .github/workflows/commands.yml:19:9:20:50 | Run Step | command13 "`command14` $(date \| wc -l)" |
-| .github/workflows/commands.yml:19:9:20:50 | Run Step | command14 |
-| .github/workflows/commands.yml:19:9:20:50 | Run Step | date |
-| .github/workflows/commands.yml:19:9:20:50 | Run Step | wc -l |
+| .github/workflows/commands.yml:15:9:18:6 | Run Step | command1 |
+| .github/workflows/commands.yml:15:9:18:6 | Run Step | command2 |
+| .github/workflows/commands.yml:18:9:20:6 | Run Step | command3 |
+| .github/workflows/commands.yml:18:9:20:6 | Run Step | command4 |
+| .github/workflows/commands.yml:20:9:22:6 | Run Step | command5 "$(command6)" |
+| .github/workflows/commands.yml:20:9:22:6 | Run Step | command6 |
+| .github/workflows/commands.yml:22:9:24:6 | Run Step | command7 |
+| .github/workflows/commands.yml:22:9:24:6 | Run Step | command8 |
+| .github/workflows/commands.yml:24:9:26:6 | Run Step | command9 |
+| .github/workflows/commands.yml:24:9:26:6 | Run Step | command10 |
+| .github/workflows/commands.yml:26:9:28:6 | Run Step | command11 "`command12`" |
+| .github/workflows/commands.yml:26:9:28:6 | Run Step | command12 |
+| .github/workflows/commands.yml:28:9:31:2 | Run Step | command13 "`command14` $(date \| wc -l)" |
+| .github/workflows/commands.yml:28:9:31:2 | Run Step | command14 |
+| .github/workflows/commands.yml:28:9:31:2 | Run Step | date |
+| .github/workflows/commands.yml:28:9:31:2 | Run Step | wc -l |
+| .github/workflows/commands.yml:34:9:37:6 | Run Step | command1 |
+| .github/workflows/commands.yml:34:9:37:6 | Run Step | command2 |
 | .github/workflows/expression_nodes.yml:7:9:8:6 | Run Step | LINE 1echo '${{ github.event.comment.body }}' |
 | .github/workflows/expression_nodes.yml:8:9:10:6 | Run Step | LINE 1 echo '${{ github.event.comment.body }}' |
 | .github/workflows/expression_nodes.yml:10:9:13:6 | Run Step | LINE 1 echo '${{ github.event.comment.body }}' |
diff --git a/ql/test/library-tests/commands.ql b/ql/test/library-tests/commands.ql
index a13608145cf..4092ac09d83 100644
--- a/ql/test/library-tests/commands.ql
+++ b/ql/test/library-tests/commands.ql
@@ -1,4 +1,4 @@
 import actions
 
 from Run run
-select run, run.getACommand()
+select run, run.getScript().getACommand()
diff --git a/ql/test/library-tests/poisonable_steps.expected b/ql/test/library-tests/poisonable_steps.expected
index 100eddb1400..a87ec0a341c 100644
--- a/ql/test/library-tests/poisonable_steps.expected
+++ b/ql/test/library-tests/poisonable_steps.expected
@@ -1,5 +1,3 @@
-| .github/workflows/multiline2.yml:63:9:66:6 | Run Step |
-| .github/workflows/multiline.yml:63:9:66:6 | Run Step |
 | .github/workflows/poisonable_steps.yml:8:9:13:6 | Uses Step |
 | .github/workflows/poisonable_steps.yml:13:9:14:6 | Run Step |
 | .github/workflows/poisonable_steps.yml:14:9:15:6 | Run Step |
diff --git a/ql/test/library-tests/test.expected b/ql/test/library-tests/test.expected
index fe5a2df8dd0..e2fb80df77f 100644
--- a/ql/test/library-tests/test.expected
+++ b/ql/test/library-tests/test.expected
@@ -1 +1,2 @@
+ERROR: Ast::ShellScript is incompatible with string (test.ql:24,66-67)
 ERROR: getCallee() cannot be resolved for type DataFlowPublic::CallNode (test.ql:62,79-88)
diff --git a/ql/test/query-tests/Security/CWE-074/.github/workflows/output1.yml b/ql/test/query-tests/Security/CWE-074/.github/workflows/output1.yml
index df583724998..01036f71148 100644
--- a/ql/test/query-tests/Security/CWE-074/.github/workflows/output1.yml
+++ b/ql/test/query-tests/Security/CWE-074/.github/workflows/output1.yml
@@ -34,5 +34,6 @@ jobs:
           name: pr_number 
       - id: clob1
         run: |
+          # VULNERABLE
           echo "OUTPUT_1=HARDCODED" >> $GITHUB_OUTPUT
           echo "OUTPUT_2=$(<pr-number)" >> $GITHUB_OUTPUT
diff --git a/ql/test/query-tests/Security/CWE-077/.github/actions/download-artifact-2/action.yaml b/ql/test/query-tests/Security/CWE-077/.github/actions/download-artifact-2/action.yaml
new file mode 100644
index 00000000000..4241647d3e1
--- /dev/null
+++ b/ql/test/query-tests/Security/CWE-077/.github/actions/download-artifact-2/action.yaml
@@ -0,0 +1,32 @@
+name: DownloadArtifacts
+description: 'Downloads and unarchives artifacts for a workflow that runs on workflow_run so that it can use its data'
+runs:
+  using: "composite"
+  steps:
+    - uses: actions/github-script@60a0d83039c74a4aee543508d2ffcb1c3799cdea # v7.0.1
+      with:
+        script: |
+          let allArtifacts = await github.rest.actions.listWorkflowRunArtifacts({
+             owner: context.repo.owner,
+             repo: context.repo.repo,
+             run_id: context.payload.workflow_run.id,
+          });
+          let matchArtifact = allArtifacts.data.artifacts.filter((artifact) => {
+            return artifact.name == "artifacts"
+          })[0];
+          let download = await github.rest.actions.downloadArtifact({
+             owner: context.repo.owner,
+             repo: context.repo.repo,
+             artifact_id: matchArtifact.id,
+             archive_format: 'zip',
+          });
+          let fs = require('fs');
+          fs.writeFileSync(`/tmp/artifacts.zip`, Buffer.from(download.data));
+    - run: |
+        mkdir -p /tmp/artifacts
+        unzip /tmp/artifacts.zip
+      shell: bash
+    - run: |
+        echo "Downloaded artifacts:"
+        ls -ablh 
+      shell: bash
diff --git a/ql/test/query-tests/Security/CWE-077/.github/actions/download-artifact/action.yaml b/ql/test/query-tests/Security/CWE-077/.github/actions/download-artifact/action.yaml
new file mode 100644
index 00000000000..0c205952102
--- /dev/null
+++ b/ql/test/query-tests/Security/CWE-077/.github/actions/download-artifact/action.yaml
@@ -0,0 +1,32 @@
+name: DownloadArtifacts
+description: 'Downloads and unarchives artifacts for a workflow that runs on workflow_run so that it can use its data'
+runs:
+  using: "composite"
+  steps:
+    - uses: actions/github-script@60a0d83039c74a4aee543508d2ffcb1c3799cdea # v7.0.1
+      with:
+        script: |
+          let allArtifacts = await github.rest.actions.listWorkflowRunArtifacts({
+             owner: context.repo.owner,
+             repo: context.repo.repo,
+             run_id: context.payload.workflow_run.id,
+          });
+          let matchArtifact = allArtifacts.data.artifacts.filter((artifact) => {
+            return artifact.name == "artifacts"
+          })[0];
+          let download = await github.rest.actions.downloadArtifact({
+             owner: context.repo.owner,
+             repo: context.repo.repo,
+             artifact_id: matchArtifact.id,
+             archive_format: 'zip',
+          });
+          let fs = require('fs');
+          fs.writeFileSync(`/tmp/artifacts.zip`, Buffer.from(download.data));
+    - run: |
+        mkdir -p /tmp/artifacts
+        unzip /tmp/artifacts.zip -d /tmp/artifacts
+      shell: bash
+    - run: |
+        echo "Downloaded artifacts:"
+        ls -ablh /tmp/artifacts
+      shell: bash
diff --git a/ql/test/query-tests/Security/CWE-077/.github/workflows/artifactpoisoning51.yml b/ql/test/query-tests/Security/CWE-077/.github/workflows/artifactpoisoning51.yml
new file mode 100644
index 00000000000..71f590fbc9c
--- /dev/null
+++ b/ql/test/query-tests/Security/CWE-077/.github/workflows/artifactpoisoning51.yml
@@ -0,0 +1,20 @@
+name: Pull Request Open
+
+on: 
+  workflow_run:
+    workflows: ["Prev"]
+    types:
+      - completed
+
+jobs:
+  Download:
+    runs-on: ubuntu-latest
+    steps:
+      - run: |
+          gh run download "${{github.event.workflow_run.id}}" --repo "${GITHUB_REPOSITORY}" --name "artifact_name"
+      - name: Unzip
+        run: |
+          unzip artifact_name.zip -d foo
+      - name: Env Var Injection
+        run: |
+          echo "pr_number=$(cat foo/bar)" >> $GITHUB_ENV
diff --git a/ql/test/query-tests/Security/CWE-077/.github/workflows/artifactpoisoning52.yml b/ql/test/query-tests/Security/CWE-077/.github/workflows/artifactpoisoning52.yml
new file mode 100644
index 00000000000..e4845a6f2f1
--- /dev/null
+++ b/ql/test/query-tests/Security/CWE-077/.github/workflows/artifactpoisoning52.yml
@@ -0,0 +1,26 @@
+name: Pull Request Open
+
+on: 
+  workflow_run:
+    workflows: ["Prev"]
+    types:
+      - completed
+
+jobs:
+  Download:
+    runs-on: ubuntu-latest
+    steps:
+      - run: |
+          gh run download "${{github.event.workflow_run.id}}" --repo "${GITHUB_REPOSITORY}" --name "artifact_name"
+      - name: Unzip
+        run: |
+          unzip artifact_name.zip -d foo
+      - name: Env Var Injection
+        run: |
+          echo "PACKAGES_FILE_LIST<<EOF" >> "${GITHUB_ENV}"
+          cat foo >> "$GITHUB_ENV"
+          echo "EOF" >> "${GITHUB_ENV}"
+
+
+
+
diff --git a/ql/test/query-tests/Security/CWE-077/.github/workflows/artifactpoisoning53.yml b/ql/test/query-tests/Security/CWE-077/.github/workflows/artifactpoisoning53.yml
new file mode 100644
index 00000000000..67209267b5c
--- /dev/null
+++ b/ql/test/query-tests/Security/CWE-077/.github/workflows/artifactpoisoning53.yml
@@ -0,0 +1,27 @@
+name: Pull Request Open
+
+on: 
+  workflow_run:
+    workflows: ["Prev"]
+    types:
+      - completed
+
+jobs:
+  Download:
+    runs-on: ubuntu-latest
+    steps:
+      - run: |
+          gh run download "${{github.event.workflow_run.id}}" --repo "${GITHUB_REPOSITORY}" --name "artifact_name"
+      - name: Unzip
+        run: |
+          unzip artifact_name.zip -d foo
+      - run: |
+          {
+            echo 'JSON_RESPONSE<<EOF'
+            cat foo
+            echo EOF
+          } >> "$GITHUB_ENV"
+
+
+
+
diff --git a/ql/test/query-tests/Security/CWE-077/.github/workflows/artifactpoisoning91.yml b/ql/test/query-tests/Security/CWE-077/.github/workflows/artifactpoisoning91.yml
new file mode 100644
index 00000000000..af9f01b572f
--- /dev/null
+++ b/ql/test/query-tests/Security/CWE-077/.github/workflows/artifactpoisoning91.yml
@@ -0,0 +1,29 @@
+name: SnapshotPR
+on:
+  workflow_run:
+    workflows:
+      - ApprovalComment
+    types:
+      - completed
+jobs:
+  snapshot:
+    permissions:
+      id-token: write
+      pull-requests: write
+      statuses: write
+    if: github.event.workflow_run.conclusion == 'success'
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@9bb56186c3b09b4f86b1c65136769dd318469633 # v4.1.2
+      - uses: ./.github/actions/download-artifact
+      - id: metadata
+        run: |
+          pr_number="$(head -n 2 /tmp/artifacts/metadata.txt | tail -n 1)"
+          pr_commit="$(tail -n 1 /tmp/artifacts/metadata.txt)"
+          echo PR_COMMIT="$pr_commit" >> "$GITHUB_ENV"
+          echo PR_NUMBER="$pr_number" >> "$GITHUB_ENV"
+      - uses: actions/checkout@9bb56186c3b09b4f86b1c65136769dd318469633 # v4.1.2
+        with:
+          ref: ${{ env.PR_COMMIT }}
+      - uses: ./.github/actions/install-deps
+      - run: make snapshot
diff --git a/ql/test/query-tests/Security/CWE-077/.github/workflows/artifactpoisoning92.yml b/ql/test/query-tests/Security/CWE-077/.github/workflows/artifactpoisoning92.yml
new file mode 100644
index 00000000000..e35bc73c3bd
--- /dev/null
+++ b/ql/test/query-tests/Security/CWE-077/.github/workflows/artifactpoisoning92.yml
@@ -0,0 +1,29 @@
+name: SnapshotPR
+on:
+  workflow_run:
+    workflows:
+      - ApprovalComment
+    types:
+      - completed
+jobs:
+  snapshot:
+    permissions:
+      id-token: write
+      pull-requests: write
+      statuses: write
+    if: github.event.workflow_run.conclusion == 'success'
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@9bb56186c3b09b4f86b1c65136769dd318469633 # v4.1.2
+      - uses: ./.github/actions/download-artifact-2
+      - id: metadata
+        run: |
+          pr_number="$(head -n 2 /tmp/artifacts/metadata.txt | tail -n 1)"
+          pr_commit="$(tail -n 1 /tmp/artifacts/metadata.txt)"
+          echo PR_COMMIT="$pr_commit" >> "$GITHUB_ENV"
+          echo PR_NUMBER="$pr_number" >> "$GITHUB_ENV"
+      - uses: actions/checkout@9bb56186c3b09b4f86b1c65136769dd318469633 # v4.1.2
+        with:
+          ref: ${{ env.PR_COMMIT }}
+      - uses: ./.github/actions/install-deps
+      - run: make snapshot
diff --git a/ql/test/query-tests/Security/CWE-077/EnvVarInjectionCritical.expected b/ql/test/query-tests/Security/CWE-077/EnvVarInjectionCritical.expected
index aff785242f9..220eaf33663 100644
--- a/ql/test/query-tests/Security/CWE-077/EnvVarInjectionCritical.expected
+++ b/ql/test/query-tests/Security/CWE-077/EnvVarInjectionCritical.expected
@@ -1,4 +1,9 @@
 edges
+| .github/actions/download-artifact-2/action.yaml:6:7:25:4 | Uses Step | .github/workflows/artifactpoisoning92.yml:20:14:24:55 | pr_number="$(head -n 2 /tmp/artifacts/metadata.txt \| tail -n 1)"\npr_commit="$(tail -n 1 /tmp/artifacts/metadata.txt)"\necho PR_COMMIT="$pr_commit" >> "$GITHUB_ENV"\necho PR_NUMBER="$pr_number" >> "$GITHUB_ENV"\n | provenance | Config |
+| .github/actions/download-artifact/action.yaml:6:7:25:4 | Uses Step | .github/workflows/artifactpoisoning91.yml:20:14:24:55 | pr_number="$(head -n 2 /tmp/artifacts/metadata.txt \| tail -n 1)"\npr_commit="$(tail -n 1 /tmp/artifacts/metadata.txt)"\necho PR_COMMIT="$pr_commit" >> "$GITHUB_ENV"\necho PR_NUMBER="$pr_number" >> "$GITHUB_ENV"\n | provenance | Config |
+| .github/workflows/artifactpoisoning51.yml:13:9:15:6 | Run Step | .github/workflows/artifactpoisoning51.yml:19:14:20:57 | echo "pr_number=$(cat foo/bar)" >> $GITHUB_ENV\n | provenance | Config |
+| .github/workflows/artifactpoisoning52.yml:13:9:15:6 | Run Step | .github/workflows/artifactpoisoning52.yml:19:14:22:40 | echo "PACKAGES_FILE_LIST<<EOF" >> "${GITHUB_ENV}"\ncat foo >> "$GITHUB_ENV"\necho "EOF" >> "${GITHUB_ENV}"\n | provenance | Config |
+| .github/workflows/artifactpoisoning53.yml:13:9:15:6 | Run Step | .github/workflows/artifactpoisoning53.yml:18:14:23:29 | {\n  echo 'JSON_RESPONSE<<EOF'\n  cat foo\n  echo EOF\n} >> "$GITHUB_ENV"\n | provenance | Config |
 | .github/workflows/test2.yml:12:9:41:6 | Uses Step | .github/workflows/test2.yml:41:14:43:52 | unzip pr.zip\necho "pr_number=$(cat NR)" >> $GITHUB_ENV\n | provenance | Config |
 | .github/workflows/test3.yml:13:7:20:4 | Uses Step | .github/workflows/test3.yml:20:12:23:77 | echo "PR_NUMBER=$(cat pr_number.txt \| jq -r .)" >> $GITHUB_ENV\necho "PR_HEAD_REPO=$(cat pr_head_repo.txt \| jq -Rr .)" >> $GITHUB_ENV\necho "PR_HEAD_REF=$(cat pr_head_ref.txt \| jq -Rr .)" >> $GITHUB_ENV\n | provenance | Config |
 | .github/workflows/test4.yml:11:19:11:56 | github.event.pull_request.title | .github/workflows/test4.yml:12:14:13:48 | echo "PR_TITLE=$TITLE" >> $GITHUB_ENV\n | provenance | Config |
@@ -25,6 +30,16 @@ edges
 | .github/workflows/test12.yml:38:9:46:6 | Uses Step | .github/workflows/test12.yml:63:14:68:29 | {\n  echo 'PRERELEASE_REPORT<<EOF'\n  cat prerelease-report.md\n  echo EOF\n} >> "$GITHUB_ENV"\n | provenance | Config |
 | .github/workflows/test12.yml:55:9:61:6 | Uses Step | .github/workflows/test12.yml:63:14:68:29 | {\n  echo 'PRERELEASE_REPORT<<EOF'\n  cat prerelease-report.md\n  echo EOF\n} >> "$GITHUB_ENV"\n | provenance | Config |
 nodes
+| .github/actions/download-artifact-2/action.yaml:6:7:25:4 | Uses Step | semmle.label | Uses Step |
+| .github/actions/download-artifact/action.yaml:6:7:25:4 | Uses Step | semmle.label | Uses Step |
+| .github/workflows/artifactpoisoning51.yml:13:9:15:6 | Run Step | semmle.label | Run Step |
+| .github/workflows/artifactpoisoning51.yml:19:14:20:57 | echo "pr_number=$(cat foo/bar)" >> $GITHUB_ENV\n | semmle.label | echo "pr_number=$(cat foo/bar)" >> $GITHUB_ENV\n |
+| .github/workflows/artifactpoisoning52.yml:13:9:15:6 | Run Step | semmle.label | Run Step |
+| .github/workflows/artifactpoisoning52.yml:19:14:22:40 | echo "PACKAGES_FILE_LIST<<EOF" >> "${GITHUB_ENV}"\ncat foo >> "$GITHUB_ENV"\necho "EOF" >> "${GITHUB_ENV}"\n | semmle.label | echo "PACKAGES_FILE_LIST<<EOF" >> "${GITHUB_ENV}"\ncat foo >> "$GITHUB_ENV"\necho "EOF" >> "${GITHUB_ENV}"\n |
+| .github/workflows/artifactpoisoning53.yml:13:9:15:6 | Run Step | semmle.label | Run Step |
+| .github/workflows/artifactpoisoning53.yml:18:14:23:29 | {\n  echo 'JSON_RESPONSE<<EOF'\n  cat foo\n  echo EOF\n} >> "$GITHUB_ENV"\n | semmle.label | {\n  echo 'JSON_RESPONSE<<EOF'\n  cat foo\n  echo EOF\n} >> "$GITHUB_ENV"\n |
+| .github/workflows/artifactpoisoning91.yml:20:14:24:55 | pr_number="$(head -n 2 /tmp/artifacts/metadata.txt \| tail -n 1)"\npr_commit="$(tail -n 1 /tmp/artifacts/metadata.txt)"\necho PR_COMMIT="$pr_commit" >> "$GITHUB_ENV"\necho PR_NUMBER="$pr_number" >> "$GITHUB_ENV"\n | semmle.label | pr_number="$(head -n 2 /tmp/artifacts/metadata.txt \| tail -n 1)"\npr_commit="$(tail -n 1 /tmp/artifacts/metadata.txt)"\necho PR_COMMIT="$pr_commit" >> "$GITHUB_ENV"\necho PR_NUMBER="$pr_number" >> "$GITHUB_ENV"\n |
+| .github/workflows/artifactpoisoning92.yml:20:14:24:55 | pr_number="$(head -n 2 /tmp/artifacts/metadata.txt \| tail -n 1)"\npr_commit="$(tail -n 1 /tmp/artifacts/metadata.txt)"\necho PR_COMMIT="$pr_commit" >> "$GITHUB_ENV"\necho PR_NUMBER="$pr_number" >> "$GITHUB_ENV"\n | semmle.label | pr_number="$(head -n 2 /tmp/artifacts/metadata.txt \| tail -n 1)"\npr_commit="$(tail -n 1 /tmp/artifacts/metadata.txt)"\necho PR_COMMIT="$pr_commit" >> "$GITHUB_ENV"\necho PR_NUMBER="$pr_number" >> "$GITHUB_ENV"\n |
 | .github/workflows/test2.yml:12:9:41:6 | Uses Step | semmle.label | Uses Step |
 | .github/workflows/test2.yml:41:14:43:52 | unzip pr.zip\necho "pr_number=$(cat NR)" >> $GITHUB_ENV\n | semmle.label | unzip pr.zip\necho "pr_number=$(cat NR)" >> $GITHUB_ENV\n |
 | .github/workflows/test3.yml:13:7:20:4 | Uses Step | semmle.label | Uses Step |
@@ -79,6 +94,11 @@ nodes
 | .github/workflows/test15.yml:18:14:20:48 | PR_BODY=$(jq --raw-output .pull_request.body ${GITHUB_EVENT_PATH})\necho "BODY=$PR_BODY" >> "$GITHUB_ENV"\n | semmle.label | PR_BODY=$(jq --raw-output .pull_request.body ${GITHUB_EVENT_PATH})\necho "BODY=$PR_BODY" >> "$GITHUB_ENV"\n |
 subpaths
 #select
+| .github/workflows/artifactpoisoning51.yml:19:14:20:57 | echo "pr_number=$(cat foo/bar)" >> $GITHUB_ENV\n | .github/workflows/artifactpoisoning51.yml:13:9:15:6 | Run Step | .github/workflows/artifactpoisoning51.yml:19:14:20:57 | echo "pr_number=$(cat foo/bar)" >> $GITHUB_ENV\n | Potential environment variable injection in $@, which may be controlled by an external user. | .github/workflows/artifactpoisoning51.yml:19:14:20:57 | echo "pr_number=$(cat foo/bar)" >> $GITHUB_ENV\n | echo "pr_number=$(cat foo/bar)" >> $GITHUB_ENV\n |
+| .github/workflows/artifactpoisoning52.yml:19:14:22:40 | echo "PACKAGES_FILE_LIST<<EOF" >> "${GITHUB_ENV}"\ncat foo >> "$GITHUB_ENV"\necho "EOF" >> "${GITHUB_ENV}"\n | .github/workflows/artifactpoisoning52.yml:13:9:15:6 | Run Step | .github/workflows/artifactpoisoning52.yml:19:14:22:40 | echo "PACKAGES_FILE_LIST<<EOF" >> "${GITHUB_ENV}"\ncat foo >> "$GITHUB_ENV"\necho "EOF" >> "${GITHUB_ENV}"\n | Potential environment variable injection in $@, which may be controlled by an external user. | .github/workflows/artifactpoisoning52.yml:19:14:22:40 | echo "PACKAGES_FILE_LIST<<EOF" >> "${GITHUB_ENV}"\ncat foo >> "$GITHUB_ENV"\necho "EOF" >> "${GITHUB_ENV}"\n | echo "PACKAGES_FILE_LIST<<EOF" >> "${GITHUB_ENV}"\ncat foo >> "$GITHUB_ENV"\necho "EOF" >> "${GITHUB_ENV}"\n |
+| .github/workflows/artifactpoisoning53.yml:18:14:23:29 | {\n  echo 'JSON_RESPONSE<<EOF'\n  cat foo\n  echo EOF\n} >> "$GITHUB_ENV"\n | .github/workflows/artifactpoisoning53.yml:13:9:15:6 | Run Step | .github/workflows/artifactpoisoning53.yml:18:14:23:29 | {\n  echo 'JSON_RESPONSE<<EOF'\n  cat foo\n  echo EOF\n} >> "$GITHUB_ENV"\n | Potential environment variable injection in $@, which may be controlled by an external user. | .github/workflows/artifactpoisoning53.yml:18:14:23:29 | {\n  echo 'JSON_RESPONSE<<EOF'\n  cat foo\n  echo EOF\n} >> "$GITHUB_ENV"\n | {\n  echo 'JSON_RESPONSE<<EOF'\n  cat foo\n  echo EOF\n} >> "$GITHUB_ENV"\n |
+| .github/workflows/artifactpoisoning91.yml:20:14:24:55 | pr_number="$(head -n 2 /tmp/artifacts/metadata.txt \| tail -n 1)"\npr_commit="$(tail -n 1 /tmp/artifacts/metadata.txt)"\necho PR_COMMIT="$pr_commit" >> "$GITHUB_ENV"\necho PR_NUMBER="$pr_number" >> "$GITHUB_ENV"\n | .github/actions/download-artifact/action.yaml:6:7:25:4 | Uses Step | .github/workflows/artifactpoisoning91.yml:20:14:24:55 | pr_number="$(head -n 2 /tmp/artifacts/metadata.txt \| tail -n 1)"\npr_commit="$(tail -n 1 /tmp/artifacts/metadata.txt)"\necho PR_COMMIT="$pr_commit" >> "$GITHUB_ENV"\necho PR_NUMBER="$pr_number" >> "$GITHUB_ENV"\n | Potential environment variable injection in $@, which may be controlled by an external user. | .github/workflows/artifactpoisoning91.yml:20:14:24:55 | pr_number="$(head -n 2 /tmp/artifacts/metadata.txt \| tail -n 1)"\npr_commit="$(tail -n 1 /tmp/artifacts/metadata.txt)"\necho PR_COMMIT="$pr_commit" >> "$GITHUB_ENV"\necho PR_NUMBER="$pr_number" >> "$GITHUB_ENV"\n | pr_number="$(head -n 2 /tmp/artifacts/metadata.txt \| tail -n 1)"\npr_commit="$(tail -n 1 /tmp/artifacts/metadata.txt)"\necho PR_COMMIT="$pr_commit" >> "$GITHUB_ENV"\necho PR_NUMBER="$pr_number" >> "$GITHUB_ENV"\n |
+| .github/workflows/artifactpoisoning92.yml:20:14:24:55 | pr_number="$(head -n 2 /tmp/artifacts/metadata.txt \| tail -n 1)"\npr_commit="$(tail -n 1 /tmp/artifacts/metadata.txt)"\necho PR_COMMIT="$pr_commit" >> "$GITHUB_ENV"\necho PR_NUMBER="$pr_number" >> "$GITHUB_ENV"\n | .github/actions/download-artifact-2/action.yaml:6:7:25:4 | Uses Step | .github/workflows/artifactpoisoning92.yml:20:14:24:55 | pr_number="$(head -n 2 /tmp/artifacts/metadata.txt \| tail -n 1)"\npr_commit="$(tail -n 1 /tmp/artifacts/metadata.txt)"\necho PR_COMMIT="$pr_commit" >> "$GITHUB_ENV"\necho PR_NUMBER="$pr_number" >> "$GITHUB_ENV"\n | Potential environment variable injection in $@, which may be controlled by an external user. | .github/workflows/artifactpoisoning92.yml:20:14:24:55 | pr_number="$(head -n 2 /tmp/artifacts/metadata.txt \| tail -n 1)"\npr_commit="$(tail -n 1 /tmp/artifacts/metadata.txt)"\necho PR_COMMIT="$pr_commit" >> "$GITHUB_ENV"\necho PR_NUMBER="$pr_number" >> "$GITHUB_ENV"\n | pr_number="$(head -n 2 /tmp/artifacts/metadata.txt \| tail -n 1)"\npr_commit="$(tail -n 1 /tmp/artifacts/metadata.txt)"\necho PR_COMMIT="$pr_commit" >> "$GITHUB_ENV"\necho PR_NUMBER="$pr_number" >> "$GITHUB_ENV"\n |
 | .github/workflows/test2.yml:41:14:43:52 | unzip pr.zip\necho "pr_number=$(cat NR)" >> $GITHUB_ENV\n | .github/workflows/test2.yml:12:9:41:6 | Uses Step | .github/workflows/test2.yml:41:14:43:52 | unzip pr.zip\necho "pr_number=$(cat NR)" >> $GITHUB_ENV\n | Potential environment variable injection in $@, which may be controlled by an external user. | .github/workflows/test2.yml:41:14:43:52 | unzip pr.zip\necho "pr_number=$(cat NR)" >> $GITHUB_ENV\n | unzip pr.zip\necho "pr_number=$(cat NR)" >> $GITHUB_ENV\n |
 | .github/workflows/test3.yml:20:12:23:77 | echo "PR_NUMBER=$(cat pr_number.txt \| jq -r .)" >> $GITHUB_ENV\necho "PR_HEAD_REPO=$(cat pr_head_repo.txt \| jq -Rr .)" >> $GITHUB_ENV\necho "PR_HEAD_REF=$(cat pr_head_ref.txt \| jq -Rr .)" >> $GITHUB_ENV\n | .github/workflows/test3.yml:13:7:20:4 | Uses Step | .github/workflows/test3.yml:20:12:23:77 | echo "PR_NUMBER=$(cat pr_number.txt \| jq -r .)" >> $GITHUB_ENV\necho "PR_HEAD_REPO=$(cat pr_head_repo.txt \| jq -Rr .)" >> $GITHUB_ENV\necho "PR_HEAD_REF=$(cat pr_head_ref.txt \| jq -Rr .)" >> $GITHUB_ENV\n | Potential environment variable injection in $@, which may be controlled by an external user. | .github/workflows/test3.yml:20:12:23:77 | echo "PR_NUMBER=$(cat pr_number.txt \| jq -r .)" >> $GITHUB_ENV\necho "PR_HEAD_REPO=$(cat pr_head_repo.txt \| jq -Rr .)" >> $GITHUB_ENV\necho "PR_HEAD_REF=$(cat pr_head_ref.txt \| jq -Rr .)" >> $GITHUB_ENV\n | echo "PR_NUMBER=$(cat pr_number.txt \| jq -r .)" >> $GITHUB_ENV\necho "PR_HEAD_REPO=$(cat pr_head_repo.txt \| jq -Rr .)" >> $GITHUB_ENV\necho "PR_HEAD_REF=$(cat pr_head_ref.txt \| jq -Rr .)" >> $GITHUB_ENV\n |
 | .github/workflows/test4.yml:12:14:13:48 | echo "PR_TITLE=$TITLE" >> $GITHUB_ENV\n | .github/workflows/test4.yml:11:19:11:56 | github.event.pull_request.title | .github/workflows/test4.yml:12:14:13:48 | echo "PR_TITLE=$TITLE" >> $GITHUB_ENV\n | Potential environment variable injection in $@, which may be controlled by an external user. | .github/workflows/test4.yml:12:14:13:48 | echo "PR_TITLE=$TITLE" >> $GITHUB_ENV\n | echo "PR_TITLE=$TITLE" >> $GITHUB_ENV\n |
diff --git a/ql/test/query-tests/Security/CWE-077/EnvVarInjectionMedium.expected b/ql/test/query-tests/Security/CWE-077/EnvVarInjectionMedium.expected
index 1ac092dd0d3..23bc7784f76 100644
--- a/ql/test/query-tests/Security/CWE-077/EnvVarInjectionMedium.expected
+++ b/ql/test/query-tests/Security/CWE-077/EnvVarInjectionMedium.expected
@@ -1,4 +1,9 @@
 edges
+| .github/actions/download-artifact-2/action.yaml:6:7:25:4 | Uses Step | .github/workflows/artifactpoisoning92.yml:20:14:24:55 | pr_number="$(head -n 2 /tmp/artifacts/metadata.txt \| tail -n 1)"\npr_commit="$(tail -n 1 /tmp/artifacts/metadata.txt)"\necho PR_COMMIT="$pr_commit" >> "$GITHUB_ENV"\necho PR_NUMBER="$pr_number" >> "$GITHUB_ENV"\n | provenance | Config |
+| .github/actions/download-artifact/action.yaml:6:7:25:4 | Uses Step | .github/workflows/artifactpoisoning91.yml:20:14:24:55 | pr_number="$(head -n 2 /tmp/artifacts/metadata.txt \| tail -n 1)"\npr_commit="$(tail -n 1 /tmp/artifacts/metadata.txt)"\necho PR_COMMIT="$pr_commit" >> "$GITHUB_ENV"\necho PR_NUMBER="$pr_number" >> "$GITHUB_ENV"\n | provenance | Config |
+| .github/workflows/artifactpoisoning51.yml:13:9:15:6 | Run Step | .github/workflows/artifactpoisoning51.yml:19:14:20:57 | echo "pr_number=$(cat foo/bar)" >> $GITHUB_ENV\n | provenance | Config |
+| .github/workflows/artifactpoisoning52.yml:13:9:15:6 | Run Step | .github/workflows/artifactpoisoning52.yml:19:14:22:40 | echo "PACKAGES_FILE_LIST<<EOF" >> "${GITHUB_ENV}"\ncat foo >> "$GITHUB_ENV"\necho "EOF" >> "${GITHUB_ENV}"\n | provenance | Config |
+| .github/workflows/artifactpoisoning53.yml:13:9:15:6 | Run Step | .github/workflows/artifactpoisoning53.yml:18:14:23:29 | {\n  echo 'JSON_RESPONSE<<EOF'\n  cat foo\n  echo EOF\n} >> "$GITHUB_ENV"\n | provenance | Config |
 | .github/workflows/test2.yml:12:9:41:6 | Uses Step | .github/workflows/test2.yml:41:14:43:52 | unzip pr.zip\necho "pr_number=$(cat NR)" >> $GITHUB_ENV\n | provenance | Config |
 | .github/workflows/test3.yml:13:7:20:4 | Uses Step | .github/workflows/test3.yml:20:12:23:77 | echo "PR_NUMBER=$(cat pr_number.txt \| jq -r .)" >> $GITHUB_ENV\necho "PR_HEAD_REPO=$(cat pr_head_repo.txt \| jq -Rr .)" >> $GITHUB_ENV\necho "PR_HEAD_REF=$(cat pr_head_ref.txt \| jq -Rr .)" >> $GITHUB_ENV\n | provenance | Config |
 | .github/workflows/test4.yml:11:19:11:56 | github.event.pull_request.title | .github/workflows/test4.yml:12:14:13:48 | echo "PR_TITLE=$TITLE" >> $GITHUB_ENV\n | provenance | Config |
@@ -25,6 +30,16 @@ edges
 | .github/workflows/test12.yml:38:9:46:6 | Uses Step | .github/workflows/test12.yml:63:14:68:29 | {\n  echo 'PRERELEASE_REPORT<<EOF'\n  cat prerelease-report.md\n  echo EOF\n} >> "$GITHUB_ENV"\n | provenance | Config |
 | .github/workflows/test12.yml:55:9:61:6 | Uses Step | .github/workflows/test12.yml:63:14:68:29 | {\n  echo 'PRERELEASE_REPORT<<EOF'\n  cat prerelease-report.md\n  echo EOF\n} >> "$GITHUB_ENV"\n | provenance | Config |
 nodes
+| .github/actions/download-artifact-2/action.yaml:6:7:25:4 | Uses Step | semmle.label | Uses Step |
+| .github/actions/download-artifact/action.yaml:6:7:25:4 | Uses Step | semmle.label | Uses Step |
+| .github/workflows/artifactpoisoning51.yml:13:9:15:6 | Run Step | semmle.label | Run Step |
+| .github/workflows/artifactpoisoning51.yml:19:14:20:57 | echo "pr_number=$(cat foo/bar)" >> $GITHUB_ENV\n | semmle.label | echo "pr_number=$(cat foo/bar)" >> $GITHUB_ENV\n |
+| .github/workflows/artifactpoisoning52.yml:13:9:15:6 | Run Step | semmle.label | Run Step |
+| .github/workflows/artifactpoisoning52.yml:19:14:22:40 | echo "PACKAGES_FILE_LIST<<EOF" >> "${GITHUB_ENV}"\ncat foo >> "$GITHUB_ENV"\necho "EOF" >> "${GITHUB_ENV}"\n | semmle.label | echo "PACKAGES_FILE_LIST<<EOF" >> "${GITHUB_ENV}"\ncat foo >> "$GITHUB_ENV"\necho "EOF" >> "${GITHUB_ENV}"\n |
+| .github/workflows/artifactpoisoning53.yml:13:9:15:6 | Run Step | semmle.label | Run Step |
+| .github/workflows/artifactpoisoning53.yml:18:14:23:29 | {\n  echo 'JSON_RESPONSE<<EOF'\n  cat foo\n  echo EOF\n} >> "$GITHUB_ENV"\n | semmle.label | {\n  echo 'JSON_RESPONSE<<EOF'\n  cat foo\n  echo EOF\n} >> "$GITHUB_ENV"\n |
+| .github/workflows/artifactpoisoning91.yml:20:14:24:55 | pr_number="$(head -n 2 /tmp/artifacts/metadata.txt \| tail -n 1)"\npr_commit="$(tail -n 1 /tmp/artifacts/metadata.txt)"\necho PR_COMMIT="$pr_commit" >> "$GITHUB_ENV"\necho PR_NUMBER="$pr_number" >> "$GITHUB_ENV"\n | semmle.label | pr_number="$(head -n 2 /tmp/artifacts/metadata.txt \| tail -n 1)"\npr_commit="$(tail -n 1 /tmp/artifacts/metadata.txt)"\necho PR_COMMIT="$pr_commit" >> "$GITHUB_ENV"\necho PR_NUMBER="$pr_number" >> "$GITHUB_ENV"\n |
+| .github/workflows/artifactpoisoning92.yml:20:14:24:55 | pr_number="$(head -n 2 /tmp/artifacts/metadata.txt \| tail -n 1)"\npr_commit="$(tail -n 1 /tmp/artifacts/metadata.txt)"\necho PR_COMMIT="$pr_commit" >> "$GITHUB_ENV"\necho PR_NUMBER="$pr_number" >> "$GITHUB_ENV"\n | semmle.label | pr_number="$(head -n 2 /tmp/artifacts/metadata.txt \| tail -n 1)"\npr_commit="$(tail -n 1 /tmp/artifacts/metadata.txt)"\necho PR_COMMIT="$pr_commit" >> "$GITHUB_ENV"\necho PR_NUMBER="$pr_number" >> "$GITHUB_ENV"\n |
 | .github/workflows/test2.yml:12:9:41:6 | Uses Step | semmle.label | Uses Step |
 | .github/workflows/test2.yml:41:14:43:52 | unzip pr.zip\necho "pr_number=$(cat NR)" >> $GITHUB_ENV\n | semmle.label | unzip pr.zip\necho "pr_number=$(cat NR)" >> $GITHUB_ENV\n |
 | .github/workflows/test3.yml:13:7:20:4 | Uses Step | semmle.label | Uses Step |
diff --git a/ql/test/query-tests/Security/CWE-829/ArtifactPoisoningCritical.expected b/ql/test/query-tests/Security/CWE-829/ArtifactPoisoningCritical.expected
index 7aa170a2e98..7a59ab6ec60 100644
--- a/ql/test/query-tests/Security/CWE-829/ArtifactPoisoningCritical.expected
+++ b/ql/test/query-tests/Security/CWE-829/ArtifactPoisoningCritical.expected
@@ -11,9 +11,6 @@ edges
 | .github/workflows/artifactpoisoning34.yml:13:9:16:6 | Run Step | .github/workflows/artifactpoisoning34.yml:20:14:22:23 | npm install\nnpm run lint\n | provenance | Config |
 | .github/workflows/artifactpoisoning41.yml:13:9:21:6 | Run Step | .github/workflows/artifactpoisoning41.yml:22:14:22:22 | ./foo/cmd | provenance | Config |
 | .github/workflows/artifactpoisoning42.yml:13:9:21:6 | Run Step | .github/workflows/artifactpoisoning42.yml:22:14:22:18 | ./cmd | provenance | Config |
-| .github/workflows/artifactpoisoning51.yml:13:9:15:6 | Run Step | .github/workflows/artifactpoisoning51.yml:19:14:20:57 | echo "pr_number=$(cat foo/bar)" >> $GITHUB_ENV\n | provenance | Config |
-| .github/workflows/artifactpoisoning52.yml:13:9:15:6 | Run Step | .github/workflows/artifactpoisoning52.yml:19:14:22:40 | echo "PACKAGES_FILE_LIST<<EOF" >> "${GITHUB_ENV}"\ncat foo >> "$GITHUB_ENV"\necho "EOF" >> "${GITHUB_ENV}"\n | provenance | Config |
-| .github/workflows/artifactpoisoning53.yml:13:9:15:6 | Run Step | .github/workflows/artifactpoisoning53.yml:18:14:23:29 | {\n  echo 'JSON_RESPONSE<<EOF'\n  cat foo\n  echo EOF\n} >> "$GITHUB_ENV"\n | provenance | Config |
 | .github/workflows/artifactpoisoning71.yml:9:9:16:6 | Uses Step | .github/workflows/artifactpoisoning71.yml:17:14:18:40 | sed -f config foo.md > bar.md\n | provenance | Config |
 | .github/workflows/artifactpoisoning81.yml:28:9:31:6 | Uses Step | .github/workflows/artifactpoisoning81.yml:31:14:31:27 | python test.py | provenance | Config |
 nodes
@@ -38,12 +35,6 @@ nodes
 | .github/workflows/artifactpoisoning41.yml:22:14:22:22 | ./foo/cmd | semmle.label | ./foo/cmd |
 | .github/workflows/artifactpoisoning42.yml:13:9:21:6 | Run Step | semmle.label | Run Step |
 | .github/workflows/artifactpoisoning42.yml:22:14:22:18 | ./cmd | semmle.label | ./cmd |
-| .github/workflows/artifactpoisoning51.yml:13:9:15:6 | Run Step | semmle.label | Run Step |
-| .github/workflows/artifactpoisoning51.yml:19:14:20:57 | echo "pr_number=$(cat foo/bar)" >> $GITHUB_ENV\n | semmle.label | echo "pr_number=$(cat foo/bar)" >> $GITHUB_ENV\n |
-| .github/workflows/artifactpoisoning52.yml:13:9:15:6 | Run Step | semmle.label | Run Step |
-| .github/workflows/artifactpoisoning52.yml:19:14:22:40 | echo "PACKAGES_FILE_LIST<<EOF" >> "${GITHUB_ENV}"\ncat foo >> "$GITHUB_ENV"\necho "EOF" >> "${GITHUB_ENV}"\n | semmle.label | echo "PACKAGES_FILE_LIST<<EOF" >> "${GITHUB_ENV}"\ncat foo >> "$GITHUB_ENV"\necho "EOF" >> "${GITHUB_ENV}"\n |
-| .github/workflows/artifactpoisoning53.yml:13:9:15:6 | Run Step | semmle.label | Run Step |
-| .github/workflows/artifactpoisoning53.yml:18:14:23:29 | {\n  echo 'JSON_RESPONSE<<EOF'\n  cat foo\n  echo EOF\n} >> "$GITHUB_ENV"\n | semmle.label | {\n  echo 'JSON_RESPONSE<<EOF'\n  cat foo\n  echo EOF\n} >> "$GITHUB_ENV"\n |
 | .github/workflows/artifactpoisoning71.yml:9:9:16:6 | Uses Step | semmle.label | Uses Step |
 | .github/workflows/artifactpoisoning71.yml:17:14:18:40 | sed -f config foo.md > bar.md\n | semmle.label | sed -f config foo.md > bar.md\n |
 | .github/workflows/artifactpoisoning81.yml:28:9:31:6 | Uses Step | semmle.label | Uses Step |
@@ -62,9 +53,6 @@ subpaths
 | .github/workflows/artifactpoisoning34.yml:20:14:22:23 | npm install\nnpm run lint\n | .github/workflows/artifactpoisoning34.yml:13:9:16:6 | Run Step | .github/workflows/artifactpoisoning34.yml:20:14:22:23 | npm install\nnpm run lint\n | Potential artifact poisoning in $@, which may be controlled by an external user. | .github/workflows/artifactpoisoning34.yml:20:14:22:23 | npm install\nnpm run lint\n | npm install\nnpm run lint\n |
 | .github/workflows/artifactpoisoning41.yml:22:14:22:22 | ./foo/cmd | .github/workflows/artifactpoisoning41.yml:13:9:21:6 | Run Step | .github/workflows/artifactpoisoning41.yml:22:14:22:22 | ./foo/cmd | Potential artifact poisoning in $@, which may be controlled by an external user. | .github/workflows/artifactpoisoning41.yml:22:14:22:22 | ./foo/cmd | ./foo/cmd |
 | .github/workflows/artifactpoisoning42.yml:22:14:22:18 | ./cmd | .github/workflows/artifactpoisoning42.yml:13:9:21:6 | Run Step | .github/workflows/artifactpoisoning42.yml:22:14:22:18 | ./cmd | Potential artifact poisoning in $@, which may be controlled by an external user. | .github/workflows/artifactpoisoning42.yml:22:14:22:18 | ./cmd | ./cmd |
-| .github/workflows/artifactpoisoning51.yml:19:14:20:57 | echo "pr_number=$(cat foo/bar)" >> $GITHUB_ENV\n | .github/workflows/artifactpoisoning51.yml:13:9:15:6 | Run Step | .github/workflows/artifactpoisoning51.yml:19:14:20:57 | echo "pr_number=$(cat foo/bar)" >> $GITHUB_ENV\n | Potential artifact poisoning in $@, which may be controlled by an external user. | .github/workflows/artifactpoisoning51.yml:19:14:20:57 | echo "pr_number=$(cat foo/bar)" >> $GITHUB_ENV\n | echo "pr_number=$(cat foo/bar)" >> $GITHUB_ENV\n |
-| .github/workflows/artifactpoisoning52.yml:19:14:22:40 | echo "PACKAGES_FILE_LIST<<EOF" >> "${GITHUB_ENV}"\ncat foo >> "$GITHUB_ENV"\necho "EOF" >> "${GITHUB_ENV}"\n | .github/workflows/artifactpoisoning52.yml:13:9:15:6 | Run Step | .github/workflows/artifactpoisoning52.yml:19:14:22:40 | echo "PACKAGES_FILE_LIST<<EOF" >> "${GITHUB_ENV}"\ncat foo >> "$GITHUB_ENV"\necho "EOF" >> "${GITHUB_ENV}"\n | Potential artifact poisoning in $@, which may be controlled by an external user. | .github/workflows/artifactpoisoning52.yml:19:14:22:40 | echo "PACKAGES_FILE_LIST<<EOF" >> "${GITHUB_ENV}"\ncat foo >> "$GITHUB_ENV"\necho "EOF" >> "${GITHUB_ENV}"\n | echo "PACKAGES_FILE_LIST<<EOF" >> "${GITHUB_ENV}"\ncat foo >> "$GITHUB_ENV"\necho "EOF" >> "${GITHUB_ENV}"\n |
-| .github/workflows/artifactpoisoning53.yml:18:14:23:29 | {\n  echo 'JSON_RESPONSE<<EOF'\n  cat foo\n  echo EOF\n} >> "$GITHUB_ENV"\n | .github/workflows/artifactpoisoning53.yml:13:9:15:6 | Run Step | .github/workflows/artifactpoisoning53.yml:18:14:23:29 | {\n  echo 'JSON_RESPONSE<<EOF'\n  cat foo\n  echo EOF\n} >> "$GITHUB_ENV"\n | Potential artifact poisoning in $@, which may be controlled by an external user. | .github/workflows/artifactpoisoning53.yml:18:14:23:29 | {\n  echo 'JSON_RESPONSE<<EOF'\n  cat foo\n  echo EOF\n} >> "$GITHUB_ENV"\n | {\n  echo 'JSON_RESPONSE<<EOF'\n  cat foo\n  echo EOF\n} >> "$GITHUB_ENV"\n |
 | .github/workflows/artifactpoisoning71.yml:17:14:18:40 | sed -f config foo.md > bar.md\n | .github/workflows/artifactpoisoning71.yml:9:9:16:6 | Uses Step | .github/workflows/artifactpoisoning71.yml:17:14:18:40 | sed -f config foo.md > bar.md\n | Potential artifact poisoning in $@, which may be controlled by an external user. | .github/workflows/artifactpoisoning71.yml:17:14:18:40 | sed -f config foo.md > bar.md\n | sed -f config foo.md > bar.md\n |
 | .github/workflows/artifactpoisoning81.yml:31:14:31:27 | python test.py | .github/workflows/artifactpoisoning81.yml:28:9:31:6 | Uses Step | .github/workflows/artifactpoisoning81.yml:31:14:31:27 | python test.py | Potential artifact poisoning in $@, which may be controlled by an external user. | .github/workflows/artifactpoisoning81.yml:31:14:31:27 | python test.py | python test.py |
 | .github/workflows/artifactpoisoning92.yml:28:9:29:6 | Uses Step | .github/actions/download-artifact-2/action.yaml:6:7:25:4 | Uses Step | .github/workflows/artifactpoisoning92.yml:28:9:29:6 | Uses Step | Potential artifact poisoning in $@, which may be controlled by an external user. | .github/workflows/artifactpoisoning92.yml:28:9:29:6 | Uses Step | Uses Step |
diff --git a/ql/test/query-tests/Security/CWE-829/ArtifactPoisoningMedium.expected b/ql/test/query-tests/Security/CWE-829/ArtifactPoisoningMedium.expected
index 8d946507799..2ed89bcb4bc 100644
--- a/ql/test/query-tests/Security/CWE-829/ArtifactPoisoningMedium.expected
+++ b/ql/test/query-tests/Security/CWE-829/ArtifactPoisoningMedium.expected
@@ -11,9 +11,6 @@ edges
 | .github/workflows/artifactpoisoning34.yml:13:9:16:6 | Run Step | .github/workflows/artifactpoisoning34.yml:20:14:22:23 | npm install\nnpm run lint\n | provenance | Config |
 | .github/workflows/artifactpoisoning41.yml:13:9:21:6 | Run Step | .github/workflows/artifactpoisoning41.yml:22:14:22:22 | ./foo/cmd | provenance | Config |
 | .github/workflows/artifactpoisoning42.yml:13:9:21:6 | Run Step | .github/workflows/artifactpoisoning42.yml:22:14:22:18 | ./cmd | provenance | Config |
-| .github/workflows/artifactpoisoning51.yml:13:9:15:6 | Run Step | .github/workflows/artifactpoisoning51.yml:19:14:20:57 | echo "pr_number=$(cat foo/bar)" >> $GITHUB_ENV\n | provenance | Config |
-| .github/workflows/artifactpoisoning52.yml:13:9:15:6 | Run Step | .github/workflows/artifactpoisoning52.yml:19:14:22:40 | echo "PACKAGES_FILE_LIST<<EOF" >> "${GITHUB_ENV}"\ncat foo >> "$GITHUB_ENV"\necho "EOF" >> "${GITHUB_ENV}"\n | provenance | Config |
-| .github/workflows/artifactpoisoning53.yml:13:9:15:6 | Run Step | .github/workflows/artifactpoisoning53.yml:18:14:23:29 | {\n  echo 'JSON_RESPONSE<<EOF'\n  cat foo\n  echo EOF\n} >> "$GITHUB_ENV"\n | provenance | Config |
 | .github/workflows/artifactpoisoning71.yml:9:9:16:6 | Uses Step | .github/workflows/artifactpoisoning71.yml:17:14:18:40 | sed -f config foo.md > bar.md\n | provenance | Config |
 | .github/workflows/artifactpoisoning81.yml:28:9:31:6 | Uses Step | .github/workflows/artifactpoisoning81.yml:31:14:31:27 | python test.py | provenance | Config |
 nodes
@@ -38,12 +35,6 @@ nodes
 | .github/workflows/artifactpoisoning41.yml:22:14:22:22 | ./foo/cmd | semmle.label | ./foo/cmd |
 | .github/workflows/artifactpoisoning42.yml:13:9:21:6 | Run Step | semmle.label | Run Step |
 | .github/workflows/artifactpoisoning42.yml:22:14:22:18 | ./cmd | semmle.label | ./cmd |
-| .github/workflows/artifactpoisoning51.yml:13:9:15:6 | Run Step | semmle.label | Run Step |
-| .github/workflows/artifactpoisoning51.yml:19:14:20:57 | echo "pr_number=$(cat foo/bar)" >> $GITHUB_ENV\n | semmle.label | echo "pr_number=$(cat foo/bar)" >> $GITHUB_ENV\n |
-| .github/workflows/artifactpoisoning52.yml:13:9:15:6 | Run Step | semmle.label | Run Step |
-| .github/workflows/artifactpoisoning52.yml:19:14:22:40 | echo "PACKAGES_FILE_LIST<<EOF" >> "${GITHUB_ENV}"\ncat foo >> "$GITHUB_ENV"\necho "EOF" >> "${GITHUB_ENV}"\n | semmle.label | echo "PACKAGES_FILE_LIST<<EOF" >> "${GITHUB_ENV}"\ncat foo >> "$GITHUB_ENV"\necho "EOF" >> "${GITHUB_ENV}"\n |
-| .github/workflows/artifactpoisoning53.yml:13:9:15:6 | Run Step | semmle.label | Run Step |
-| .github/workflows/artifactpoisoning53.yml:18:14:23:29 | {\n  echo 'JSON_RESPONSE<<EOF'\n  cat foo\n  echo EOF\n} >> "$GITHUB_ENV"\n | semmle.label | {\n  echo 'JSON_RESPONSE<<EOF'\n  cat foo\n  echo EOF\n} >> "$GITHUB_ENV"\n |
 | .github/workflows/artifactpoisoning71.yml:9:9:16:6 | Uses Step | semmle.label | Uses Step |
 | .github/workflows/artifactpoisoning71.yml:17:14:18:40 | sed -f config foo.md > bar.md\n | semmle.label | sed -f config foo.md > bar.md\n |
 | .github/workflows/artifactpoisoning81.yml:28:9:31:6 | Uses Step | semmle.label | Uses Step |